Genetic and QTL analyses of sink size traits in pearl millet(Pennisetum glaucum (L.) R. Br.)

Present study was carried out to characterize the genetic architecture of three sink size component traits (panicle length, panicle diameter and grain size) through genetic and QTL analyses. The plant materials for genetic analysis consisted of two crosses for the generation means and variance analyses, and one cross for triple test cross (TTC) analysis for each of three traits. The material for QTL analysis consisted of 188 F2 and their F2:3 progeny mapping populations of a cross between the two inbred lines. The plant materials were developed during the 2005-06 and the field experiments were conducted during the 2006 rainy and 2007 summer seasons. Scaling and joint scaling tests revealed that a simplistic additive-dominance model did not adequately explain the observed variation for all the three traits in both seasons, providing an evidence for the presence of epistasis. The six-parameter model and the TTC analysis revealed significance of both additive and dominance effects for cross 1 of panicle length, panicle diameter and grain size. However, cross 2 of panicle length and panicle diameter revealed only additive effects and grain size showed the presence of both additive and dominance gene effects. All three types of interactions (additive x additive, additive x dominance and dominance x dominance) were found to be significant in cross 1 for all the traits across seasons using generation means analysis. However, TTC analysis revealed the presence of all types of epistasis for panicle length and panicle diameter. For grain size, it revealed the presence of only additive x dominance and dominance x dominance (j + l) epistasis. In cross 2, additive x additive (i) interaction alone was significant for panicle length and panicle diameter, whereas for grain size, dominance x dominance (l) followed by additive x dominance (j) contributed significantly across seasons. The estimates of broad and narrow-sense heritability were high for all the traits. Correlation coefficient estimates revealed that panicle length, panicle diameter and grain size were positively and significantly associated with grain yield in their respective trait-specific crosses. The linkage map constructed using 44 markers (SNP, SSR, EST-SSR and STS markers) with 188 F2:3 progenies had a total length of 1018.7 cM. The average distance between the marker pairs was 23 cM. QTL analysis performed as composite interval mapping (CIM) identified eight genomic regions for panicle length, one each on LG 1, 2, 4 and 7; and two each on LG 3 and 6. The variation explained by these QTLs ranged from 6.1 to 18.2%. For panicle diameter, five QTLs were found across LG 2, 3, 5, 6 and 7 and the variation explained by these individual QTLs ranged from 6.3 to 30.2%. For grain size also five QTLs were identified across LG 1, 3, 5, 6 and 7 and the individual QTLs explained 6.1 to 21.2% of the observed phenotypic variation across F2 and F2:3 data sets. From the mapped QTLs, one QTL on LG 2 for panicle length, two QTLs each on LG 2 and 3 for panicle diameter and one QTL on LG 3 for grain size are identified as candidate QTLs for marker-assisted selection.