Identification of genomic regions and candidate genes for seed weight and fresh seed dormancy in groundnut
Creators: name: Gangurde, Sunil S.
Publisher: name: Zenodo
Year: 2023
Subjects: Peanut, Groundnut, Seed weight, Fresh seed dormancy, candidate genes, Diagnostic markers

description: Seed weight is an important yield-related trait for achieving high production and bold<br> seeded groundnut is preferred by consumers. Lack of fresh seed dormancy (FSD)<br> hampers the yield as well as quality of seeds. Therefore in present study, we tried<br> genetic dissection of groundnut seed weight and FSD using bi-parental and multi parental<br> populations. In addition, sequencing-based trait mapping approach called<br> ‘QTL-seq’ by sequencing the extreme bulks to discover the genomic regions and<br> candidate genes associated with seed weight and FSD.<br> For mapping the genomic regions for seed weight, a bi-parental population (Chico ×<br> ICGV 02251) and two nested association mapping (NAM) populations (NAMTifrunner<br> and NAM-Florida-07) were phenotyped for two seasons for seed, pod<br> weights and shelling percentage. However, for mapping the genomic regions for FSD a<br> RIL population (ICGV 00350 × ICGV 97045) was phenotyped for fresh seed<br> dormancy. The bi-parental and multi-parental populations used for seed weight were<br> genotyped using 58K ‘Axiom_Arachis’ SNP array to construct a dense genetic map and<br> to discover the genomic regions. To perform QTL-Seq analysis for FSD, two extreme<br> bulks respectively for dormant and non-dormant RILs were constructed on the basis of<br> phenotyping data recorded on RIL population (ICGV 00350 × ICGV 97045). However,<br> to perform QTL-Seq analysis for seed weight, two extreme bulks respectively for small<br> seed weight and large seed weight was constructed on the basis of phenotyping data<br> generated for seed weight on RIL population (Chico × ICGV 02251) phenotyped for<br> fresh seed dormancy and extreme bulks were constructed to perform sequencing based<br> bulk segregant analysis. For seed weight, genetic mapping and QTL analysis identified two QTLs on<br> chromosome A04 with phenotypic variance 14.4% and 17.1%. Stable QTLs for<br> shelling percentage were identified on chromosomes A05, A08 and B10 with<br> phenotypic variance explained (PVE) of 11.0%, 9.0% and 12.0% respectively.<br> Important genes such as BEG SEED locus and spermidine synthase were identified on<br> chromosomes A09 and B09. Nested association mapping for seed weight identified<br> major QTLs for seed weight on chromosomes A05, A06, B05, and B06. A genome-wide<br> association study (GWAS) analysis identified highly significant SNP-trait associations (STAs) for PW and SW. These significant STAs were co-localized on<br> similar positions as the detected QTLs, suggesting that PW and SW are regulated by<br> common set of candidate genes identified on chromosomes A05, A06, B05, and B06.<br> Interestingly, QTL-Seq analysis for seed weight identified five genomic regions (three<br> on B06, one each on B08 and B09) for seed weight. Sequence analysis of above<br> associated genomic regions identified a total of 180 SNPs in genic and intergenic<br> regions. 11 of these SNPs were non-synonymous and located in the coding region of 10<br> candidate genes playing important role in regulation of seed weight. Diagnostic<br> Kompetitive Allele Specific PCR (KASP) markers were developed successfully for 14<br> SNPs from genomic regions of important candidate genes and four of these markers<br> could be successfully validated in groundnut genotypes with contrasting seed weight.<br> In case of FSD, whole genome sequencing (WGS) data (87.93 Gbp) was generated at<br> high depth and analyzed for the ICGV 97045 (dormant parent) and two DNA bulks,<br> dormant (D-bulk) and non-dormant bulk (ND-bulk). A total of 10,759 genome-wide<br> SNPs were discovered by comparing the sequencing data of both bulks with reference<br> genome. In depth QTL-Seq analysis identified two candidate genomic regions spanning<br> a distance of 2.4 Mb and 0.74 Mb on chromosome B05 and A09 respectively<br> controlling FSD. Two candidate genes RING-H2 finger protein and zeaxanthin<br> epoxidase were identified in these two regions, found to be significantly expressed<br> during seed development and control abscisic acid (ABA) accumulation in seed. A<br> diagnostic allele specific marker GMFSD1 and 6 KASP markers were successfully<br> developed from the genomic region on chromosome A09 and B05 and validated on<br> diverse FSD genotypes.