BACKGROUND
wheat  is one the world’s major staple crops, supplying approximately twenty percent of the global total calorie intake .
there have been considerable advances in yield since the introduction of the ‘green revolution’ genes.
however for the uk, europe and other countries worldwide, the last decade has seen a decline in the rate of genetic gains, with yield plateaus in some environments .
furthermore, with the global demand for wheat rising faster than the rate of yield improvement, there is a genuine threat to food security.
therefore the discovery, understanding and eventual incorporation of genes and alleles that beneficially influence yield are major targets for breeding programs worldwide.
the grain yield of wheat and cereals in general, is a polygenic and highly complex trait that is influenced by environmental and genetic interactions at all stages of the plant’s growth .
to facilitate its study, yield is usually broken down into three main components; number of spikes per surface area, grain number per spike, and thousand grain weight .
these yield components are sequentially fixed during the growth cycle, vary in terms of their heritability, and are not always positively correlated with yield .
tgw is usually stably inherited  and can be further broken down into individual components including physical parameters  and grain filling characteristics, which are also under independent genetic control .
these include both the rate and duration of the grain filling process , the latter being normally phenotyped as green canopy duration after heading .
in the past decade, there have been significant advances in our understanding of the genetic control of grain size, shape, and grain filling parameters in the diploid crop species rice .
several genes with relatively large effects have been identified through map-based cloning and support the independent genetic control of grain length, width and grain filling parameters.
this differs from our limited understanding in polyploid wheat where several studies have identified quantitative trait loci  for grain size and shape , but no gene has yet been cloned.
moreover, many of these qtl are in relatively wide genomic regions and have not been validated and fine-mapped using independent germplasm, therefore having limited impact in breeding.
in rice, osgw <dig> encodes a previously unknown ring-type e <dig> ubiquitin ligase and functions as a negative regulator of grain width and weight .
recently, several studies have examined the role of the wheat homologue  on grain size parameters, although contradictory results have been reported.
two studies have described a snp at position − <dig> upstream of the putative start codon as significantly associated with wider grains and increased tgw in chinese germplasm .
however, the results are directly contradictory since each study found the positive association with the opposite snp at the exact − <dig> position.
despite the alternative alleles at this site, both studies identify a negative association between tagw <dig> expression levels and grain width.
yang et al.
identified a tagw <dig> frame-shift mutation in a large-kernel variety, and associated this mutant allele with increased grain width and tgw in a large f2: <dig> population.
this mutant mimics the original rice osgw <dig> truncation allele , suggesting that tagw <dig> and osgw <dig> share a conserved mechanism .
however, down-regulation of tagw <dig> through rna interference  resulted in decreased grain size and tgw in wheat , suggesting that tagw <dig> is a positive regulator of grain size with a divergent function to that of rice osgw <dig>  taken together, it is difficult to conclude the exact effect of tagw <dig> on grain size and tgw in wheat due to the discrepant studies published to date.
the objective of this study was to evaluate a doubled haploid mapping population across north european environments for thousand grain weight, yield and additional morphological and developmental traits.
we identified a meta-qtl for tgw, yield, and green canopy duration on wheat chromosome 6a.
we developed near isogenic lines  to validate the 6a qtl effects across environments, and morphometric grain analyses were conducted to determine the specific grain size components being affected by the qtl.
RESULTS
genetic map and qtl analyses
the spark x rialto dh linkage map was developed using  <dig> markers, including  <dig> ssrs,  <dig> dart,  <dig> protein markers, the rht-d1b perfect marker, and a morphological ga test.
the total length of the map was  <dig>  cm across  <dig> linkage groups which were assigned to specific chromosomes using published consensus maps .
seven chromosomes included at least two linkage groups  which were considered separately for the qtl analyses.
across locations, rialto had significantly  larger thousand grain weight  than spark  and this was consistent across years .
in the dh population, five qtl for grain size were consistently identified across at least five locations on chromosomes 1b, 2a, 2d, 4d and 6a .
the rialto allele conferred the increased grain size for four qtl , whereas spark provided the increased grain size on chromosome 4d.
two qtl for yield were identified across environments on chromosomes 4d and 6a, and both co-localized with the previously identified thousand grain weight qtl .
the 4d yield and tgw qtl peaks coincide with the rht-d <dig> dwarfing gene whose pleiotropic effect on yield and yield components has been comprehensively documented .
the yield and tgw qtl on chromosome 6a were detected between markers xgdm <dig> and xgwm <dig> with rialto providing the increasing allele for both traits.
this chromosome region was the only one apart from rht-d <dig> that significantly influenced both yield and grain weight in the spark × rialto dh population.
therefore, the grain size and yield qtl on chromosome 6a were selected for further study and designated as qtgw-jic.6a and qyld-jic.6a, respectively.
a factorial anova was conducted including environment and all two-way interactions to assess individual qtl effects and epistatic interactions between rht-d <dig> and qtgw-jic.6a/qyld-jic.6a.
there was a significant effect of rht-d <dig> and the 6a qtl on tgw  and yield  and strong interactions between qtl and environment for both traits .
however, there was no significant genetic interaction between rht-d <dig> and qtgw-jic.6a/qyld-jic.6a .
dh lines homozygous for the 6a rialto region between xgdm <dig> and xgwm <dig> had a significant increase in yield of  <dig>  ±  <dig> % across environments compared to dh fixed for the spark allele .
these gains ranged from  <dig> %  to  <dig> % .
increases in tgw were more variable, averaging  <dig>  ±  <dig> % and ranging from  <dig> %  to  <dig> %  .
the mean yield and tgw for the selected dh lines at each environment were positively correlated , although this was not significant  due to differential effects across environments.
for example, dh lines fixed for the qyld-jic.6a rialto segment exhibited yield improvements of  <dig> % in scotland , however tgw was only increased by  <dig> % at this site , whereas in other environments  tgw and yield were significantly correlated .
these results suggest that tgw is an important yield component underlying the qyld-jic.6a effect, however, the relative contribution of increased tgw on yield varied across environments.
in addition to the tgw and yield effects, a qtl for green canopy duration after heading  was also identified between xgdm <dig> and xgwm <dig> and designated qgcd-jic.6a.
similar to qtgw-jic.6a and qyld-jic.6a, the rialto allele had the positive effect extending green canopy duration significantly by  <dig>  ±  <dig>  days  compared to the spark allele, across all four environments analysed.
green canopy duration showed a significant  negative correlation with yield across the four locations , although the correlations were not significant in three of the four environments.
there was no significant correlation  between green canopy duration and tgw  across environments.
chromosome 6a had no effect on plant biomass, harvest index, seeds/spike, and seeds/spikelet across locations.
multi-trait multi-environment qtl analyses
the marker resolution across chromosome 6a was increased by the addition of  <dig> snp-based markers .
the improved 6a genetic map covers a genetic distance of 66 cm, ranging from xgwm <dig> at the distal end of the short arm, to xgwm <dig> which maps mid-way along the long arm .
using the improved genetic map for chromosome 6a, the original phenotypic data was reanalysed using multi-trait multi-environment  analysis for a more precise positioning of the qtl across all environments .
for yield, qyld-jic.6a was identified as significant across the interval from xgdm <dig>  to xgwm <dig> , with the peak at wpt- <dig>  .
significant markers within this region were identified in  <dig> of the  <dig> environments, all with rialto as the beneficial allele .
for qtgw-jic.6a the qtl encompasses the whole linkage group with all markers showing significance and with rialto providing the positive allele in all cases.
the qtl reaches its highest significance between wpt- <dig>  to xgwm <dig> , with the peak at be <dig> .
significant markers were observed in all environments apart from france and germany in  <dig> .
qgcd-jic.6a spans the region from be <dig>  to be <dig> , has its highest significance at xgwm <dig>  and was significant across all four environments .
the mtme analysis established that the yield, tgw and green canopy duration effects are all co-localised to a 8 cm region between wpt- <dig>  to xgwm <dig>  and that these effects are stable across different north european environments.
in addition to these major effects, a minor qtl for tiller number was identified at bq <dig>  in three of the five environments , mapping distal to the location of qyld-jic.6a, qtgw-jic.6a and qgcd-jic.6a.
in this case, however, spark provided the positive effect allele.
validation of qtgw-jic.6a and qyld-jic.6a using near isogenic lines
to independently validate these multiple effects, bc <dig> and bc <dig> nils segregating for the qtl segment  were developed.
nils were assessed for yield, tgw and grain size parameters in five environments, four in england  and one in germany  .
overall, the rialto 6a nil significantly increased yield , although there was a strong interaction with environment .
in four of the five experiments yield increases were observed from the rialto nils , with three of these effects being significant and one non-significant .
however, a significant decrease in plot yield was observed in  <dig> in england, where rialto nils had  <dig> % lower yield .
for tgw, a significant increase was observed in rialto nils across locations , although again there was a significant interaction with environment  .
similar to plot yield, rialto increased tgw in four environments  with three being significant and one borderline non-significant .
no effects on tgw were observed in  <dig>  the plot yield and tgw of the 6a nils was positively correlated  across environments.
similar to the dh population, no consistent differences were observed between nils for plant biomass, harvest index, spike length, spikelet number, spike yield, seeds/spike, and seeds/spikelet .
2
and bc
4
nils
performance of nils with either the recurrent parent  or the introgressed region  across  <dig> environments.
significant differences are represented by * , **  and *** ; non-significant effects are also indicated .
delta refers to the difference between the rialto and spark nil phenotypes as a percentage of the spark nil.
morphometric measurements of the grain were analysed to assess the source of the increases in tgw .
total grain area was significantly increased in four of the five environments in an equivalent degree to the tgw results.
this was expected based on the high positive correlation between these two measures .
the increased grain size and weight was due primarily to significantly wider grains in the rialto nils.
grains from rialto nils were on average  <dig> % wider than grains from spark nils  and this was highly significant in four of the five environments tested.
no significant effect in grain length was observed between nils across locations with the exception of  <dig> where rialto nils had significantly longer grains than spark nils .
the alignment of twenty grains of equivalent bc lines illustrates the difference in grain width between bc <dig> and bc <dig> nils and the variation in grain size across environments .
validation of developmental traits using nils
developmental characteristics including heading date, physiological maturity and the calculation of green canopy duration were assessed in the uk environment over four years using bc <dig>  and bc <dig>  nils.
despite extreme variation in growing conditions over this period, robust significant effects were observed for all three traits .
for heading date, nils containing the rialto introgression flowered earlier by  <dig>  ±  <dig>  days .
rialto nils also were significantly later at reaching physiological maturity compared to spark nils in all four seasons by  <dig>  ±  <dig>  days .
the combination of these two effects significantly lengthens the green canopy duration for the rialto nils by an average of  <dig>  ±  <dig>  days across environments .
the non-significant interaction  between green canopy duration and environment highlights the consistent effect of the rialto allele across growing seasons, despite the large variation in average green canopy duration between years .
these results suggest that the original green canopy duration qtl qgcd-jic.6a is in fact a combination of two distinct effects, earlier flowering and delayed final maturity, which both co-localize to the 6a region and are stably expressed across environments.
2
and bc
4
nils
heading and maturity are calculated as the number of days from drilling, whereas green canopy duration is determined by the difference between heading and maturity dates.
significant differences are represented by *, ** and ***; non-significant effects are also indicated .
delta refers to the difference between the rialto and spark nil phenotypes in absolute values.
quantitative spad measurements were taken from the flag leaves of bc <dig> nils in  <dig> and  <dig> to confirm the qualitative plot assessments and measure the rate of senescence .
in both years, no significant differences were observed in relative chlorophyll content at 20– <dig> days after anthesis .
significant differences, however, were detected at  <dig> daa in  <dig>  and at  <dig> daa in  <dig>  with spark nils showing significantly lower relative chlorophyll content in flag leaves compared to the rialto nils.
tiller number were assessed from  <dig> to  <dig> and again highlighted the large variation in growing seasons with numbers ranging from a mean of  <dig>  tillers per m row in  <dig> to  <dig>  in  <dig> .
significantly fewer tillers were recorded in the higher yielding rialto nils in both  <dig>  and  <dig> , but not  <dig>  no significant correlations were observed between tiller number, yield and tgw in all three years.
2
nils.
spad units of nils carrying the rialto  or spark  6a interval in  <dig>  and  <dig>  after anthesis.
significant differences are represented by * , **  and *** .
sequence analysis of tagw2
in rice, the ring-type e <dig> ubiquitin ligase osgw <dig> has been shown to negatively affect grain width.
the wheat homologue tagw <dig> has been mapped to chromosome 6a  and was, therefore, considered as a potential candidate gene for qtgw-jic.6a .
rialto, which produced wider grains and increased tgw and yield was found to contain the g allele at the − <dig> promoter snp.
using this polymorphism, tagw <dig> was mapped on the spark x rialto dh population to chromosome 6a co-locating with markers bs <dig>  bs <dig> and ca <dig> at  <dig>  cm , within the 8 cm peak interval determined by mtme .
sequencing of tagw <dig> gdna revealed only the single snp at position − <dig> of the  <dig>  bp upstream of the start codon between spark and rialto.
no additional polymorphisms were detected in the a-genome coding sequence nor in the splice sites between spark and rialto.
likewise, no snps or alternative splicing variants were identified for the a-genome from spark and rialto cdna samples.
discussion
the interplay between tgw/yield/green canopy duration
qtl analysis of the spark x rialto dh population demonstrated the co-localisation of qtl determining green canopy duration, grain size  and grain yield within an 8 cm interval on chromosome 6a.
these effects were confirmed with the development and assessment of independent nils of the rialto region into the spark background.
it was established that the extension of the green canopy duration qgcd-jic.6a was comprised of two independent traits, both earlier flowering and a delay in the final senescence which resulted in a significant extension of the green canopy duration.
both component traits mapped to the rialto 6a introgression, but their genetic relationship  could not be established with the germplasm used in this study.
green canopy duration after heading is commonly, yet mistakenly, used interchangeably with extended grain filling duration.
this common generalisation leads many studies to conclude that extended green canopy duration leads to extended grain filling duration thereby resulting in larger grains and increased yield .
we have shown, however, that this is not a direct/causal relationship in all cases.
caution should be exercised when interpreting the outcome of delayed leaf and plant senescence, especially in the absence of direct measurements on grain moisture content and maturity.
for example, rnai lines for the gpc gene confer an extended green canopy duration of >25 days , yet this is not accompanied by an extension in grain filling duration per se .
the results of our current study also suggest that this mechanism is not the main driver behind the rialto 6a yield effect.
qgcd-jic.6a showed no correlation with yield or tgw in the dh population, and despite a significant difference in gcd between nils in  <dig>  no yield or grain size benefit was observed.
this suggests that qgcd-jic.6a is most likely an independent genetic locus within the introgressed region , and that extended gcd is not the major determinant behind the increase in productivity observed in the dh population and nils.
although the relative magnitude of effects between grain size and yield were not always consistent, a significant positive correlation was observed between the two traits across environments, suggesting that grain weight is most likely the principal yield component for qyld-jic.6a.
in four of the five nil validation experiments the rialto introgression gave significant improvements in yield  and tgw , with morphometric measurements showing that the increased grain weight was predominantly a result of wider grains.
the final weight of individual grains is the last of the yield components to be established once the number of spikes per surface area and the grain number per spike have already been fixed .
this close correlation between grain weight and yield provides what could be seen as a more precise route to increased yields, compared to manipulating other yield components, as it is stably inherited  and compensatory effects are limited.
given the current rate of genetic gain in hexaploid wheat breeding, the >5% yield effect is equivalent to ~10 years of breeding, without considering additional phenotypic variation which could be identified in homoeologous loci for the 6a qtl.
ultimately, fine mapping though recombinant inbred lines will assist in determining the precise location of the traits discussed here and determine if the yield effect is pleiotropic to grain weight .
compared to the large number of qtl studies for yield and other complex traits in wheat, there have been relatively few studies into individual grain morphometric components.
ramya et al.
identified several independent genetic loci for tgw and grain length and width in a large dh population, with four of these qtl suggested as pleiotropic for tgw and length/width parameters.
in the current study we did not assess the original dh population for grain morphometric parameters due to the laborious nature of this task when the original field trials were conducted .
however, with the development of high throughout phenotyping equipment, such as the marvin grain analyzer, we were able to assess the nils in greater detail and determine the most likely effect underlying the increase tgw.
these new phenotyping tools should greatly facilitate the genetic dissection of grain size parameters in wheat in the coming years.
absence of yield and tgw effect in 2012
in the  <dig> uk growing environment no effect was seen in tgw and a negative response to yield was observed in the rialto nils despite the otherwise consistent positive effects in the additional four environments.
a possible explanation for this inconsistent result is the presence of an undesirable minor qtl for tiller number within the rialto introgressed region that maps distal to the grain size and yield effects.
we detected a minor qtl in the dh lines using the mtme analysis in three of the five environments tested, although this effect was borderline significant .
similar effects of lower tiller number in rialto nils were observed in  <dig> and 2013; however, they only affected the expression of the 6a yield and tgw effects in  <dig>  this growing season was uncharacteristic in the uk due to extreme weather contrasts.
the winter of  <dig> and spring of  <dig> were relatively warm and dry compared to the uk historical averages, leading to high levels of tiller production; however this was followed by an exceptionally wet period from april through much of the summer.
specifically for the 6a nils, we observed a two-fold increase in tiller number compared to the averages of the  <dig> and  <dig> seasons.
it is plausible that the higher tiller number in  <dig> led to additional genetic x environment interactions and compensatory effects in the nils which affected the expression of the 6a tgw and yield qtl.
tagw <dig> as a potential candidate gene for qyld-jic.6a and qtgw-jic.6a
the mtme qtl analysis defined an 8 cm region between wpt- <dig>  and xgwm <dig>  in which both qyld-jic.6a and qtgw-jic.6a co-localised.
within this region we mapped tagw <dig>  the wheat homologue of osgw <dig>  loss of function of osgw <dig> in rice leads to increased cell numbers in the spikelet hull , resulting in wider grains and indirectly affecting grain filling rates .
the combined effects lead to a 50% higher tgw in nils with the loss of function osgw <dig> allele, and multiple other pleiotropic effects.
in first instance, the similarity of effects between qyld-jic.6a/qtgw-jic.6a and osgw <dig> on tgw and grain width, and their syntenic positions in wheat and rice, respectively, suggests that tagw <dig> is a compelling candidate gene for qyld-jic.6a/qtgw-jic.6a.
there are several results, however, which suggest a cautious approach is needed in evaluating the possible role of tagw <dig> as qyld-jic.6a/qtgw-jic.6a.
first, the effect of qtgw-jic.6a on tgw is relatively small compared to that seen in rice , with nils carrying the positive effect qtl interval showing between  <dig> and 9% higher tgw.
this could be in part due to the polyploid nature of hexaploid wheat, with the additional homoeologues resulting in a dosage effect causing the phenotype variation to be more subtle.
second, the direct effect of osgw <dig> is on palea and lemma cell number which would be less relevant in the case of wheat due to the small role that these structures play on grain width and size.
third, the allelic variation at the sequence level between the spark and rialto parents is limited to a sole snp in the promoter region which has been loosely associated with tgw and width although with contradictory results .
perhaps the best evidence that tagw <dig> does indeed affect tgw and grain width in polyploid wheat comes from yang et al.
and bednarek et al.
who show the effect through a frame-shift mutation and rnai, respectively.
however, their results point to opposite effects for tagw <dig>  it is too early to conclude if and how tagw <dig> affects grain width and tgw in the spark x rialto population, but several additional experiments including detailed expression analysis and the fine mapping of qyld-jic.6a/qtgw-jic.6a with respect to tagw <dig> will help elucidate this relationship.
genetic architecture of quantitative traits in wheat
in rice, the grain size qtls identified from bi-parental mapping populations have relatively large effects on tgw and yield, whereas in wheat the majority of studies have identified qtl with relatively small additive effects on grain size .
these differences could be due to several reasons.
first, the biological mechanisms determining grain size and yield might be different across species.
for example, several rice qtl affect grain size indirectly through the modulation of spikelet hull and glume size .
these indirect effects might be species-specific since in wheat, the palea and lemma  are not so firmly attached to the grain and most likely do not determine its growth in the same manner as in rice.
second, the polyploid nature of wheat means that in many cases, mutations in individual homoeologues can be masked by functional complementation with homoeologous genes present in the other genomes.
this redundancy suggests that for many genes in wheat, their full effect will only be quantifiable when all two/three homoeologues are simultaneously mutated.
this problem is further confounded for quantitative traits where multiple genes contribute to a specific phenotype.
a cloned qtl for grain protein content in wheat  exemplifies the effect of polyploidy on the relative magnitude of a quantitative trait.
the original mapping of the qtl identified phenotypic variation in grain protein content between nils of approximately 10% .
the cloning of the gene, allowed simultaneous down-regulation of the different homoeologues using rnai, and revealed a much larger effect in grain protein content  than that of the b-genome homoeologue alone .
recently, this dosage effect has been confirmed in homozygous ems-mutants of the a and d genome homoeologues.
individual gene knockouts of the gpc-a <dig> and gpc-d <dig> homoeologues had a relatively small effect on grain protein content , whereas the double mutant had a significantly larger reduction of 17% .
future directions
the validation of these qtl using nils provides a critical first step to further fine map both traits using a series of homozygous recombinant lines.
the recent advances in wheat and triticeae genomics provide a robust framework from which to identify additional markers and candidate genes to aid in this process.
these advances include the public release of the wheat chromosome arm survey sequence by the international wheat genome sequencing consortium , the development of high throughput snp assays , exome sequencing of tilling populations , and the ongoing progress on individual chromosome arm physical maps .
however, to fully exploit these genomic advances, a shift from a quantitative to a qualitative genetic locus will ultimately be required to isolate the gene underlying these grain size and yield effects.
CONCLUSIONS
in this study we identified major and stable qtl for yield, grain weight, and green canopy duration in polyploid wheat across north european environments.
these effects were validated using a series of nils which showed, on average, over 5% improvement in yield and tgw in four of the five environments tested.
our results suggest that the yield effect is driven primarily by increased grain weight due to wider grains.
the lack of correlation between prolonged green canopy duration and yield/tgw argue against a direct/causal relationship between these traits within the germplasm studied.
using a promoter polymorphism, we mapped the tagw <dig> candidate gene within the qtl interval, although it is still premature to assign a specific contribution of this gene to the qtl effect.
the validation of this qtl provides an important first step to advance our understanding of the genetic mechanisms regulating the complex processes governing grain size and yield in polyploid wheat.

 wheat is one the world’s major staple crops, supplying approximately twenty percent of the global total calorie intake. there have been considerable advances in yield since the introduction of the ‘green revolution’ genes. however for the uk, europe and other countries worldwide, the last decade has seen a decline in the rate of genetic gains, with yield plateaus in some environments. furthermore, with the global demand for wheat rising faster than the rate of yield improvement, there is a genuine threat to food security. therefore the discovery, understanding and eventual incorporation of genes and alleles that beneficially influence yield are major targets for breeding programs worldwide. the grain yield of wheat and cereals in general, is a polygenic and highly complex trait that is influenced by environmental and genetic interactions at all stages of the plant’s growth. to facilitate its study, yield is usually broken down into three main components; number of spikes per surface area, grain number per spike, and thousand grain weight. these yield components are sequentially fixed during the growth cycle, vary in terms of their heritability, and are not always positively correlated with yield. tgw is usually stably inherited and can be further broken down into individual components including physical parameters and grain filling characteristics, which are also under independent genetic control. these include both the rate and duration of the grain filling process, the latter being normally phenotyped as green canopy duration after heading. in the past decade, there have been significant advances in our understanding of the genetic control of grain size, shape, and grain filling parameters in the diploid crop species rice. several genes with relatively large effects have been identified through map-based cloning and support the independent genetic control of grain length, width and grain filling parameters. this differs from our limited understanding in polyploid wheat where several studies have identified quantitative trait loci for grain size and shape, but no gene has yet been cloned. moreover, many of these qtl are in relatively wide genomic regions and have not been validated and fine-mapped using independent germplasm, therefore having limited impact in breeding. in rice, osgw encodes a previously unknown ring-type e ubiquitin ligase and functions as a negative regulator of grain width and weight. recently, several studies have examined the role of the wheat homologue on grain size parameters, although contradictory results have been reported. two studies have described a snp at position − upstream of the putative start codon as significantly associated with wider grains and increased tgw in chinese germplasm. however, the results are directly contradictory since each study found the positive association with the opposite snp at the exact − position. despite the alternative alleles at this site, both studies identify a negative association between tagw expression levels and grain width. yang et al. identified a tagw frame-shift mutation in a large-kernel variety, and associated this mutant allele with increased grain width and tgw in a large f2: population. this mutant mimics the original rice osgw truncation allele, suggesting that tagw and osgw share a conserved mechanism. however, down-regulation of tagw through rna interference resulted in decreased grain size and tgw in wheat, suggesting that tagw is a positive regulator of grain size with a divergent function to that of rice osgw taken together, it is difficult to conclude the exact effect of tagw on grain size and tgw in wheat due to the discrepant studies published to date. the objective of this study was to evaluate a doubled haploid mapping population across north european environments for thousand grain weight, yield and additional morphological and developmental traits. we identified a meta-qtl for tgw, yield, and green canopy duration on wheat chromosome 6a. we developed near isogenic lines to validate the 6a qtl effects across environments, and morphometric grain analyses were conducted to determine the specific grain size components being affected by the qtl.  genetic map and qtl analyses the spark x rialto dh linkage map was developed using markers, including ssrs, dart, protein markers, the rht-d1b perfect marker, and a morphological ga test. the total length of the map was  cm across linkage groups which were assigned to specific chromosomes using published consensus maps. seven chromosomes included at least two linkage groups which were considered separately for the qtl analyses. across locations, rialto had significantly larger thousand grain weight than spark and this was consistent across years. in the dh population, five qtl for grain size were consistently identified across at least five locations on chromosomes 1b, 2a, 2d, 4d and 6a. the rialto allele conferred the increased grain size for four qtl, whereas spark provided the increased grain size on chromosome 4d. two qtl for yield were identified across environments on chromosomes 4d and 6a, and both co-localized with the previously identified thousand grain weight qtl. the 4d yield and tgw qtl peaks coincide with the rht-d dwarfing gene whose pleiotropic effect on yield and yield components has been comprehensively documented. the yield and tgw qtl on chromosome 6a were detected between markers xgdm and xgwm with rialto providing the increasing allele for both traits. this chromosome region was the only one apart from rht-d that significantly influenced both yield and grain weight in the spark × rialto dh population. therefore, the grain size and yield qtl on chromosome 6a were selected for further study and designated as qtgw-jic.6a and qyld-jic.6a, respectively. a factorial anova was conducted including environment and all two-way interactions to assess individual qtl effects and epistatic interactions between rht-d and qtgw-jic.6a/qyld-jic.6a. there was a significant effect of rht-d and the 6a qtl on tgw and yield and strong interactions between qtl and environment for both traits. however, there was no significant genetic interaction between rht-d and qtgw-jic.6a/qyld-jic.6a. dh lines homozygous for the 6a rialto region between xgdm and xgwm had a significant increase in yield of  ±  % across environments compared to dh fixed for the spark allele. these gains ranged from % to %. increases in tgw were more variable, averaging  ±  % and ranging from % to %. the mean yield and tgw for the selected dh lines at each environment were positively correlated, although this was not significant due to differential effects across environments. for example, dh lines fixed for the qyld-jic.6a rialto segment exhibited yield improvements of % in scotland, however tgw was only increased by % at this site, whereas in other environments tgw and yield were significantly correlated. these results suggest that tgw is an important yield component underlying the qyld-jic.6a effect, however, the relative contribution of increased tgw on yield varied across environments. in addition to the tgw and yield effects, a qtl for green canopy duration after heading was also identified between xgdm and xgwm and designated qgcd-jic.6a. similar to qtgw-jic.6a and qyld-jic.6a, the rialto allele had the positive effect extending green canopy duration significantly by  ±   days compared to the spark allele, across all four environments analysed. green canopy duration showed a significant negative correlation with yield across the four locations, although the correlations were not significant in three of the four environments. there was no significant correlation between green canopy duration and tgw across environments. chromosome 6a had no effect on plant biomass, harvest index, seeds/spike, and seeds/spikelet across locations. multi-trait multi-environment qtl analyses the marker resolution across chromosome 6a was increased by the addition of snp-based markers. the improved 6a genetic map covers a genetic distance of 66 cm, ranging from xgwm at the distal end of the short arm, to xgwm which maps mid-way along the long arm. using the improved genetic map for chromosome 6a, the original phenotypic data was reanalysed using multi-trait multi-environment analysis for a more precise positioning of the qtl across all environments. for yield, qyld-jic.6a was identified as significant across the interval from xgdm to xgwm, with the peak at wpt-. significant markers within this region were identified in of the environments, all with rialto as the beneficial allele. for qtgw-jic.6a the qtl encompasses the whole linkage group with all markers showing significance and with rialto providing the positive allele in all cases. the qtl reaches its highest significance between wpt- to xgwm, with the peak at be. significant markers were observed in all environments apart from france and germany in. qgcd-jic.6a spans the region from be to be, has its highest significance at xgwm and was significant across all four environments. the mtme analysis established that the yield, tgw and green canopy duration effects are all co-localised to a 8 cm region between wpt- to xgwm and that these effects are stable across different north european environments. in addition to these major effects, a minor qtl for tiller number was identified at bq in three of the five environments, mapping distal to the location of qyld-jic.6a, qtgw-jic.6a and qgcd-jic.6a. in this case, however, spark provided the positive effect allele. validation of qtgw-jic.6a and qyld-jic.6a using near isogenic lines to independently validate these multiple effects, bc and bc nils segregating for the qtl segment were developed. nils were assessed for yield, tgw and grain size parameters in five environments, four in england and one in germany. overall, the rialto 6a nil significantly increased yield, although there was a strong interaction with environment. in four of the five experiments yield increases were observed from the rialto nils, with three of these effects being significant and one non-significant. however, a significant decrease in plot yield was observed in in england, where rialto nils had % lower yield. for tgw, a significant increase was observed in rialto nils across locations, although again there was a significant interaction with environment. similar to plot yield, rialto increased tgw in four environments with three being significant and one borderline non-significant. no effects on tgw were observed in the plot yield and tgw of the 6a nils was positively correlated across environments. similar to the dh population, no consistent differences were observed between nils for plant biomass, harvest index, spike length, spikelet number, spike yield, seeds/spike, and seeds/spikelet. 2 and bc 4 nils performance of nils with either the recurrent parent or the introgressed region across environments. significant differences are represented by *, ** and ***; non-significant effects are also indicated. delta refers to the difference between the rialto and spark nil phenotypes as a percentage of the spark nil. morphometric measurements of the grain were analysed to assess the source of the increases in tgw. total grain area was significantly increased in four of the five environments in an equivalent degree to the tgw results. this was expected based on the high positive correlation between these two measures. the increased grain size and weight was due primarily to significantly wider grains in the rialto nils. grains from rialto nils were on average % wider than grains from spark nils and this was highly significant in four of the five environments tested. no significant effect in grain length was observed between nils across locations with the exception of where rialto nils had significantly longer grains than spark nils. the alignment of twenty grains of equivalent bc lines illustrates the difference in grain width between bc and bc nils and the variation in grain size across environments. validation of developmental traits using nils developmental characteristics including heading date, physiological maturity and the calculation of green canopy duration were assessed in the uk environment over four years using bc and bc nils. despite extreme variation in growing conditions over this period, robust significant effects were observed for all three traits. for heading date, nils containing the rialto introgression flowered earlier by  ±   days. rialto nils also were significantly later at reaching physiological maturity compared to spark nils in all four seasons by  ±   days. the combination of these two effects significantly lengthens the green canopy duration for the rialto nils by an average of  ±   days across environments. the non-significant interaction between green canopy duration and environment highlights the consistent effect of the rialto allele across growing seasons, despite the large variation in average green canopy duration between years. these results suggest that the original green canopy duration qtl qgcd-jic.6a is in fact a combination of two distinct effects, earlier flowering and delayed final maturity, which both co-localize to the 6a region and are stably expressed across environments. 2 and bc 4 nils heading and maturity are calculated as the number of days from drilling, whereas green canopy duration is determined by the difference between heading and maturity dates. significant differences are represented by *, ** and ***; non-significant effects are also indicated. delta refers to the difference between the rialto and spark nil phenotypes in absolute values. quantitative spad measurements were taken from the flag leaves of bc nils in and to confirm the qualitative plot assessments and measure the rate of senescence. in both years, no significant differences were observed in relative chlorophyll content at 20– days after anthesis. significant differences, however, were detected at daa in and at daa in with spark nils showing significantly lower relative chlorophyll content in flag leaves compared to the rialto nils. tiller number were assessed from to and again highlighted the large variation in growing seasons with numbers ranging from a mean of tillers per m row in to in. significantly fewer tillers were recorded in the higher yielding rialto nils in both and, but not no significant correlations were observed between tiller number, yield and tgw in all three years. 2 nils. spad units of nils carrying the rialto or spark 6a interval in and after anthesis. significant differences are represented by *, ** and ***. sequence analysis of tagw2 in rice, the ring-type e ubiquitin ligase osgw has been shown to negatively affect grain width. the wheat homologue tagw has been mapped to chromosome 6a and was, therefore, considered as a potential candidate gene for qtgw-jic.6a. rialto, which produced wider grains and increased tgw and yield was found to contain the g allele at the − promoter snp. using this polymorphism, tagw was mapped on the spark x rialto dh population to chromosome 6a co-locating with markers bs bs and ca at  cm, within the 8 cm peak interval determined by mtme. sequencing of tagw gdna revealed only the single snp at position − of the  bp upstream of the start codon between spark and rialto. no additional polymorphisms were detected in the a-genome coding sequence nor in the splice sites between spark and rialto. likewise, no snps or alternative splicing variants were identified for the a-genome from spark and rialto cdna samples. discussion the interplay between tgw/yield/green canopy duration qtl analysis of the spark x rialto dh population demonstrated the co-localisation of qtl determining green canopy duration, grain size and grain yield within an 8 cm interval on chromosome 6a. these effects were confirmed with the development and assessment of independent nils of the rialto region into the spark background. it was established that the extension of the green canopy duration qgcd-jic.6a was comprised of two independent traits, both earlier flowering and a delay in the final senescence which resulted in a significant extension of the green canopy duration. both component traits mapped to the rialto 6a introgression, but their genetic relationship could not be established with the germplasm used in this study. green canopy duration after heading is commonly, yet mistakenly, used interchangeably with extended grain filling duration. this common generalisation leads many studies to conclude that extended green canopy duration leads to extended grain filling duration thereby resulting in larger grains and increased yield. we have shown, however, that this is not a direct/causal relationship in all cases. caution should be exercised when interpreting the outcome of delayed leaf and plant senescence, especially in the absence of direct measurements on grain moisture content and maturity. for example, rnai lines for the gpc gene confer an extended green canopy duration of >25 days, yet this is not accompanied by an extension in grain filling duration per se. the results of our current study also suggest that this mechanism is not the main driver behind the rialto 6a yield effect. qgcd-jic.6a showed no correlation with yield or tgw in the dh population, and despite a significant difference in gcd between nils in no yield or grain size benefit was observed. this suggests that qgcd-jic.6a is most likely an independent genetic locus within the introgressed region, and that extended gcd is not the major determinant behind the increase in productivity observed in the dh population and nils. although the relative magnitude of effects between grain size and yield were not always consistent, a significant positive correlation was observed between the two traits across environments, suggesting that grain weight is most likely the principal yield component for qyld-jic.6a. in four of the five nil validation experiments the rialto introgression gave significant improvements in yield and tgw, with morphometric measurements showing that the increased grain weight was predominantly a result of wider grains. the final weight of individual grains is the last of the yield components to be established once the number of spikes per surface area and the grain number per spike have already been fixed. this close correlation between grain weight and yield provides what could be seen as a more precise route to increased yields, compared to manipulating other yield components, as it is stably inherited and compensatory effects are limited. given the current rate of genetic gain in hexaploid wheat breeding, the >5% yield effect is equivalent to ~10 years of breeding, without considering additional phenotypic variation which could be identified in homoeologous loci for the 6a qtl. ultimately, fine mapping though recombinant inbred lines will assist in determining the precise location of the traits discussed here and determine if the yield effect is pleiotropic to grain weight. compared to the large number of qtl studies for yield and other complex traits in wheat, there have been relatively few studies into individual grain morphometric components. ramya et al. identified several independent genetic loci for tgw and grain length and width in a large dh population, with four of these qtl suggested as pleiotropic for tgw and length/width parameters. in the current study we did not assess the original dh population for grain morphometric parameters due to the laborious nature of this task when the original field trials were conducted. however, with the development of high throughout phenotyping equipment, such as the marvin grain analyzer, we were able to assess the nils in greater detail and determine the most likely effect underlying the increase tgw. these new phenotyping tools should greatly facilitate the genetic dissection of grain size parameters in wheat in the coming years. absence of yield and tgw effect in 2012 in the uk growing environment no effect was seen in tgw and a negative response to yield was observed in the rialto nils despite the otherwise consistent positive effects in the additional four environments. a possible explanation for this inconsistent result is the presence of an undesirable minor qtl for tiller number within the rialto introgressed region that maps distal to the grain size and yield effects. we detected a minor qtl in the dh lines using the mtme analysis in three of the five environments tested, although this effect was borderline significant. similar effects of lower tiller number in rialto nils were observed in and 2013; however, they only affected the expression of the 6a yield and tgw effects in this growing season was uncharacteristic in the uk due to extreme weather contrasts. the winter of and spring of were relatively warm and dry compared to the uk historical averages, leading to high levels of tiller production; however this was followed by an exceptionally wet period from april through much of the summer. specifically for the 6a nils, we observed a two-fold increase in tiller number compared to the averages of the and seasons. it is plausible that the higher tiller number in led to additional genetic x environment interactions and compensatory effects in the nils which affected the expression of the 6a tgw and yield qtl. tagw as a potential candidate gene for qyld-jic.6a and qtgw-jic.6a the mtme qtl analysis defined an 8 cm region between wpt- and xgwm in which both qyld-jic.6a and qtgw-jic.6a co-localised. within this region we mapped tagw the wheat homologue of osgw loss of function of osgw in rice leads to increased cell numbers in the spikelet hull, resulting in wider grains and indirectly affecting grain filling rates. the combined effects lead to a 50% higher tgw in nils with the loss of function osgw allele, and multiple other pleiotropic effects. in first instance, the similarity of effects between qyld-jic.6a/qtgw-jic.6a and osgw on tgw and grain width, and their syntenic positions in wheat and rice, respectively, suggests that tagw is a compelling candidate gene for qyld-jic.6a/qtgw-jic.6a. there are several results, however, which suggest a cautious approach is needed in evaluating the possible role of tagw as qyld-jic.6a/qtgw-jic.6a. first, the effect of qtgw-jic.6a on tgw is relatively small compared to that seen in rice, with nils carrying the positive effect qtl interval showing between and 9% higher tgw. this could be in part due to the polyploid nature of hexaploid wheat, with the additional homoeologues resulting in a dosage effect causing the phenotype variation to be more subtle. second, the direct effect of osgw is on palea and lemma cell number which would be less relevant in the case of wheat due to the small role that these structures play on grain width and size. third, the allelic variation at the sequence level between the spark and rialto parents is limited to a sole snp in the promoter region which has been loosely associated with tgw and width although with contradictory results. perhaps the best evidence that tagw does indeed affect tgw and grain width in polyploid wheat comes from yang et al. and bednarek et al. who show the effect through a frame-shift mutation and rnai, respectively. however, their results point to opposite effects for tagw it is too early to conclude if and how tagw affects grain width and tgw in the spark x rialto population, but several additional experiments including detailed expression analysis and the fine mapping of qyld-jic.6a/qtgw-jic.6a with respect to tagw will help elucidate this relationship. genetic architecture of quantitative traits in wheat in rice, the grain size qtls identified from bi-parental mapping populations have relatively large effects on tgw and yield, whereas in wheat the majority of studies have identified qtl with relatively small additive effects on grain size. these differences could be due to several reasons. first, the biological mechanisms determining grain size and yield might be different across species. for example, several rice qtl affect grain size indirectly through the modulation of spikelet hull and glume size. these indirect effects might be species-specific since in wheat, the palea and lemma are not so firmly attached to the grain and most likely do not determine its growth in the same manner as in rice. second, the polyploid nature of wheat means that in many cases, mutations in individual homoeologues can be masked by functional complementation with homoeologous genes present in the other genomes. this redundancy suggests that for many genes in wheat, their full effect will only be quantifiable when all two/three homoeologues are simultaneously mutated. this problem is further confounded for quantitative traits where multiple genes contribute to a specific phenotype. a cloned qtl for grain protein content in wheat exemplifies the effect of polyploidy on the relative magnitude of a quantitative trait. the original mapping of the qtl identified phenotypic variation in grain protein content between nils of approximately 10%. the cloning of the gene, allowed simultaneous down-regulation of the different homoeologues using rnai, and revealed a much larger effect in grain protein content than that of the b-genome homoeologue alone. recently, this dosage effect has been confirmed in homozygous ems-mutants of the a and d genome homoeologues. individual gene knockouts of the gpc-a and gpc-d homoeologues had a relatively small effect on grain protein content, whereas the double mutant had a significantly larger reduction of 17%. future directions the validation of these qtl using nils provides a critical first step to further fine map both traits using a series of homozygous recombinant lines. the recent advances in wheat and triticeae genomics provide a robust framework from which to identify additional markers and candidate genes to aid in this process. these advances include the public release of the wheat chromosome arm survey sequence by the international wheat genome sequencing consortium, the development of high throughput snp assays, exome sequencing of tilling populations, and the ongoing progress on individual chromosome arm physical maps. however, to fully exploit these genomic advances, a shift from a quantitative to a qualitative genetic locus will ultimately be required to isolate the gene underlying these grain size and yield effects.  in this study we identified major and stable qtl for yield, grain weight, and green canopy duration in polyploid wheat across north european environments. these effects were validated using a series of nils which showed, on average, over 5% improvement in yield and tgw in four of the five environments tested. our results suggest that the yield effect is driven primarily by increased grain weight due to wider grains. the lack of correlation between prolonged green canopy duration and yield/tgw argue against a direct/causal relationship between these traits within the germplasm studied. using a promoter polymorphism, we mapped the tagw candidate gene within the qtl interval, although it is still premature to assign a specific contribution of this gene to the qtl effect. the validation of this qtl provides an important first step to advance our understanding of the genetic mechanisms regulating the complex processes governing grain size and yield in polyploid wheat. 
in this study we identified a major qtl for tgw, yield and green canopy duration on wheat chromosome 6a of the spark x rialto population, across north european environments. using independent germplasm in the form of bc and bc near isogenic lines, we validated the three qtl effects across environments. the discovery and validation through near-isogenic lines of robust qtl which affect yield, green canopy duration, thousand grain weight, and grain width on chromosome 6a of hexaploid wheat provide an important first step to advance our understanding of the genetic mechanisms regulating the complex processes governing grain size and yield in polyploid wheat. the wheat homologue of a rice gene associated with increased tgw and grain width was mapped within the qtl interval. the extended green canopy duration associated with the high yielding/tgw rialto allele was comprised of two independent effects; earlier flowering and delayed final maturity, and was expressed stably across the five environments. in four of the five experiments the rialto 6a introgression gave significant improvements in yield and tgw, with morphometric measurements showing that the increased grain weight was a result of wider grains. in polyploid wheat, studies have identified quantitative trait loci which affect tgw, yet few have been validated and fine-mapped using independent germplasm, thereby having limited impact in breeding. yield is usually broken down into three components; number of spikes per area, grain number per spike, and grain weight. grain yield in wheat is a polygenic trait that is influenced by environmental and genetic interactions at all stages of the plant’s growth.
 grain yield in wheat is a polygenic trait that is influenced by environmental and genetic interactions at all stages of the plant’s growth. yield is usually broken down into three components; number of spikes per area, grain number per spike, and grain weight. in polyploid wheat, studies have identified quantitative trait loci which affect tgw, yet few have been validated and fine-mapped using independent germplasm, thereby having limited impact in breeding.  in this study we identified a major qtl for tgw, yield and green canopy duration on wheat chromosome 6a of the spark x rialto population, across north european environments. using independent germplasm in the form of bc and bc near isogenic lines, we validated the three qtl effects across environments. in four of the five experiments the rialto 6a introgression gave significant improvements in yield and tgw, with morphometric measurements showing that the increased grain weight was a result of wider grains. the extended green canopy duration associated with the high yielding/tgw rialto allele was comprised of two independent effects; earlier flowering and delayed final maturity, and was expressed stably across the five environments. the wheat homologue of a rice gene associated with increased tgw and grain width was mapped within the qtl interval. however, no polymorphisms were identified in the coding sequence between the parents.  the discovery and validation through near-isogenic lines of robust qtl which affect yield, green canopy duration, thousand grain weight, and grain width on chromosome 6a of hexaploid wheat provide an important first step to advance our understanding of the genetic mechanisms regulating the complex processes governing grain size and yield in polyploid wheat. wheatyieldgrain sizegrain shapegreen canopy durationqtlnils 