DOI: 10.5061/dryad.s7h44j1g7
title: Data from: QTL mapping genotype and phenotype data, Vanilla x MCM5001

description: Pod quality and yield traits in snap bean (Phaseolus vulgaris L.)
 influence consumer preferences, crop adoption by farmers, and the ability
 of the product to be commercially competitive locally and globally. The
 objective of the study was to identify the quantitative trait loci (QTL)
 for pod quality and yield traits in a snap × dry bean recombinant inbred
 line (RIL) population. A total of 184 F6 RILs derived from a cross between
 Vanilla (snap bean) and MCM5001 (dry bean) were grown in three field sites
 in Kenya and one greenhouse environment in Davis, CA, USA. They were
 genotyped at 5,951 single nucleotide polymorphisms (SNPs), and composite
 interval mapping was conducted to identify QTL for 16 pod quality and
 yield traits, including pod wall fiber, pod string, pod size, and harvest
 metrics. A combined total of 44 QTL were identified in field and
 greenhouse trials. The QTL for pod quality were identified on chromosomes
 Pv01, Pv02, Pv03, Pv04, Pv06, and Pv07, and for pod yield were identified
 on Pv08. Co-localization of QTL was observed for pod quality and yield
 traits. Some identified QTL overlapped with previously mapped QTL for pod
 quality and yield traits, with several others identified as novel. The
 identified QTL can be used in future marker-assisted selection in snap
 bean.
description: A biparental mapping population of 184 F6 recombinant inbred
 lines (RILs) derived from a cross between Vanilla (female parent) and
 MCM5001 was used for linkage mapping and QTL analysis. Vanilla snap bean
 is produced by the Vilmorin Company in France
 (https://www.vilmorinmikado.fr/haricots/vanilla) and cultivated in Kenya,
 mainly for export. The variety has white seeds, fine market class pods
 (6-9 mm in diameter), and is resistance to bean common mosaic virus
 (BCMV), halo blight (Pseudomonas syringae pv. phaseolicola), and rust
 (Uromyces appendiculatus). MCM5001 is a dry bush bean bred for resistance
 to BCMV and bean common mosaic necrosis virus (BCMNV) by the International
 Center for Tropical Agriculture (CIAT, Cali, Colombia). Its seed are brown
 and cream speckled. The RILs were developed through single seed descent
 (SSD) in an insect-free greenhouse at the University of Embu (37° 27’ E,
 0° 30’ S). <em> Plant growth
 conditions</em> The 184 RILs and their parents
 were evaluated in three field sites in Kenya: (i) Kutus farm in Kirinyaga
 County (37° 19’ E, 0° 33’ S; 1,279 masl), (ii) Don Bosco farm in Embu
 County (37° 29’ E, 0° 34’ S; 1,259 masl), and (iii) Mariira farm in
 Murang’a County (36° 56’ E, 0° 47’ S; 1,255 masl), as well as in a
 greenhouse at the University of California, Davis (121° 45’ W, 38° 32’ N).
 In the greenhouse, seeds of the parents and RILs were sown in pots filled
 with 5 kg topsoil. The soils for the Kutus and Mariira farms were
 classified as Humic Nitisols while at Don Bosco there were Nito- Rhodic
 Ferralsols. The three trials were conducted during the short rain season
 of 2022 and supplemented with irrigation. The field trials were conducted
 in randomized complete block designs (RCBD) with three replications, while
 the greenhouse experiment was a completely randomized design (CRD) with a
 single replicate. In the field, each RIL and the parents were planted in a
 single row plot, measuring 2 m long at a spacing of 20 cm between the
 plants and 50 cm between the rows. The fields were plowed and harrowed to
 achieve a moderate tilth seedbed. Di-ammonium phosphate (18- 46-0)
 fertilizer was applied at a rate of 200 kg ha-1 and thoroughly mixed with
 soil. During flowering, the plants were top-dressed with calcium ammonium
 nitrate (27-0-0) at a rate of 100 kg ha-1. All cultural practices were
 conducted to ensure that the fields were free of pests, diseases, and
 weeds. <em>Phenotypic data
 collection</em> Eight snap bean traits were
 evaluated (pod wall fiber, pod string, pod diameter, pod length, pod
 weight per plant, pod number per plant, pod shape and pod shattering),
 although pod string and pod wall fiber were evaluated using more than one
 criterion for both the field and greenhouse conditions as shown in Table
 1. Unique codes were assigned to differentiate between the data gathered
 in the greenhouse and the data collected in the field in Table 1. Data on
 pod wall fiber for dry pods were collected at the R9 stage (pod
 maturation; Fernández et al., 1985) while fresh pods were examined at the
 R8 stage (pod fill). Ten pods were sampled in the greenhouse and in the
 field, a total of 30 pods were sampled per site (10 from each
 replication). The dry pod fiber was first evaluated for presence or
 absence of constrictions and secondly based on a scale of 0 (no wall
 fiber) to 10 (full wall fiber). The fresh pods were snapped in the middle
 to determine the presence or absence of fibers on a scale of 0-2 (0-no
 fiber, 1-few fibers and 2-many fibers). The pod string
 was also evaluated for both fresh and dry pods. The fresh pods that were
 obtained from the field were boiled in a water bath for 30 minutes at
 100°C. The pod strings were gently pulled from the calyx along the adaxial
 suture of the length of the detached string, measured and recorded. The
 fresh pod string length was then calculated as a ratio of pod suture
 string length to total pod length (Hagerty et al., 2016). Pod diameter
 (PD) was measured by passing the pods through holes of a bean pod ruler
 manufactured by Royal Sluis®. The holes vary in diameter sizes ranging
 from 5 mm to 9 mm. The pod length (PL) was measured from the end of the
 petiole to the tip of the pod while the pod weight per plant (PWPP) was
 computed by dividing the total weight of the pods by the number of plants.
 Pods per plant (PPP) was computed by dividing the total number of pods by
 the number of plants. <em>Phenotypic data
 analysis</em> Statistical analyses on
 quantitative phenotypic data were conducted in SAS 9.3 (SAS Institute
 2011). Normality of the data was assessed by Shapiro-Wilk test and
 outliers were treated accordingly before proceeding with analysis of
 variance (ANOVA). A combined ANOVA for the three sites was, therefore,
 conducted using PROC GLM for the traits based on the following statistical
 model: Yijkl = μ+pi + tj + bk(i) + ptij +
 eijkl where: Yijkl = Response variable; μ = Mean of the
 population; Q26 pi = Fixed effect of the ith site; tj = Fixed effect of
 the jth genotype (RILs); bk(i) = Random effect of the kth replication
 within ith site; ptij = Fixed effect due to the interaction between ith
 site and jth genotype; eijkl= Residual effect.
 Quantitative data were compared between traits based on Spearman
 correlation coefficients and plots were generated in R (R Core Team, 2022)
 using the packages tidyverse (Wickham et al., 2019), corrplot (Wei and
 Simko, 2021), and psych (Revelle, 2024). Heritabilities and variance
 partitioning analyses were conducted on field data using the heritability
 R package (Kruijer et al., 2023). Furthermore, independent t-tests were
 conducted to compare relationships between qualitative and quantitative
 traits, while Fisher’s Exact tests were conducted to show the association
 between qualitative traits. The analyses were conducted in R (R Core Team,
 2022). <em>Genotyping, linkage mapping, and QTL
 analysis</em> Single nucleotide polymorphism
 (SNP) genotyping was accomplished by genotyping-by-sequencing (Elshire et
 al., 2011; Ariani et al., 2016). DNA was extracted from greenhouse-grown
 seeds of the RILs and parents using Qiagen DNeasy extraction kit (Qiagen,
 Hilden, Germany). DNA quality was checked by NanoDrop spectrophotometer
 and agarose gel electrophoresis. Library prep was conducted with CviAII
 and 150 bp paired-end sequencing was conducted on the prepared libraries
 at the University of California, Davis Genome Center. The reads were
 aligned with the v2.1 reference genome assembly of G19833 (Goodstein et
 al., 2013; Schmutz et al., 2014;
 https://phytozome-next.jgi.doe.gov/info/Pvulgaris_v2_1).
 Read demultiplexing, alignment to the common bean reference
 genome (G19833 v2.1 (Schmutz et al., 2014), and variant calling was
 conducted in NGSEP3 and NGSEP4 (Tello et al., 2019, Tello et al., 2024).
 Data curation was performed by removing SNPs with more than 20% missing or
 heterozygous calls. SNPs were only kept if they had a genotype quality
 (GQ) over 20, were biallelic, had a minor allele frequency &gt; 0.25,
 were at least 5 bp from any other SNP, were genotyped in at least 160 of
 184 population members, and were found in non-repetitive regions, as
 defined by Lobaton et al. (2018). Individuals were plotted by missing
 calls and by heterozygous calls, and outliers were eliminated from further
 analysis. Non-parental alleles were removed. Only SNPs that were
 polymorphic in both the parents and the RIL population and had minor
 allele frequencies (MAFs) &gt;0.25, were used for linkage mapping.
 After the quality checks, 5,951 SNPs were retained for linkage map
 construction. Linkage mapping was conducted in Rstudio using the ASMap R
 package (Taylor and Butler, 2017). QTL mapping was conducted using maximum
 likelihood through the EM algorithm of the R/qtl package in R (Lander and
 Botstein, 1989; Broman et al., 2003). The genetic distances were
 calculated based on Kosambi mapping function. A significant LOD score
 threshold for QTL (LOD=3.413) was developed based on the 95th percentile
 of LOD scores of 1000 random permutations of the genotypic data. A total
 of 11 linkage groups corresponding to the 11 chromosomes were developed.
 The coefficient of determination (R2) was used to estimate the proportion
 of variation explained by a QTL (1-10^ (-(2/n)*LOD) where n is the number
 of individuals genotyped at the locus. All traits were initially
 considered as quantitative variables for QTL mapping. For the traits with
 no continuous distribution the lines were grouped in phenotypic classes
 considering the parental phenotype and verifying the SNP-trait
 associations by Fisher’s Exact tests. Results were compared with gene
 models located between flanking SNPs in v2.1 of the common bean reference
 genome (Schmutz et al., 2014). 
description: # QTL mapping genotype and phenotype data, Vanilla x MCM5001 This is
 phenotypic and genotypic data on an F6 recombinant inbred population of
 Phaseolus vulgaris. The parent lines are Vanilla (a snap bean) and MCM5001
 (a dry bean). Sixteen phenotypic traits were measured in the population,
 and the lines were genotyped using genotyping by sequencing.  Data is
 formatted to be read into R/qtl (Broman et al., 2003;
 10.1093/bioinformatics/btg112). Briefly, phenotypic data is found to the
 left of the column with sample names, and genotype data is found to the
 right of this sample name column. "-" is used in the phenotype
 sections when there was missing data, or in the case of missing or
 homozygous data in the genotype section. Two rows above the phenotype data
 and sample names are left intentionally blank, as these are only for
 linkage group and linkage distance (cM) of the genotype data, per R/qtl
 formatting. **Phenotype data explanation:** Pod shape (PS): 0= round; 1=
 flat Pod length (PLF): Measured in cm Pod suture string scale (PSSS): 0-10
 scale. 0= minimum string, 10=maximum string Pod fiber scale (PFS):  0-10
 scale. 0= minimum fiber, 10= maximum fiber Pod suture string (PSS): 0=
 minimum string, 1=maximum string Pod wall fiber (PWF):  0= no fiber; 1=
 fiber Pod shattering (PSH): 0= no shattering, 1 = shattering Pod weight
 per plant (PWPP): Measured in grams Pods per plant (PPP): Count of pods
 per plant Pod length (PL): Measured in cm Pod diameter (PD): Measured in
 mm Pod string fresh pods (PSFP):  0= no string; 1= string Pod fiber fresh
 pods (PFFP): 0-2 scale. 0= minimum fiber; 2 = maximum fiber Pod shape
 (PSh): 0-1 scale. 0 = round, 1= flat Pod string dry pods (PSDP):  0-10
 scale. 0= minimum string, 10=maximum string Pod fiber dry pods (PFDP):
 0-10 scale. 0= minimum, 10=maximum See Njau et al. 2024 "QTL mapping
 for pod quality and yield traits in snap bean (*Phaseolus vulgaris*
 L.)", *Frontiers in Plant Sciences*, for more
 information: [https://doi.org/10.5061/dryad.s7h44j1g7](https://doi.org/10.5061/dryad.s7h44j1g7)