Genome-Wide DArTSeq Genotyping and Phenotypic Based Assessment of Within and Among Accessions Diversity and Effective Sample Size in the Diverse Sorghum, Pearl Millet, and Pigeonpea Landraces

Abstract

Germplasm should be conserved in such a way that the genetic integrity of a given accession is maintained. In most genebanks, landraces constitute a major portion of collections, wherein the extent of genetic diversity within and among landraces of crops vary depending on the extent of outcrossing and selection intensity infused by farmers. In this study, we assessed the level of diversity within and among 108 diverse landraces and wild accessions using both phenotypic and genotypic characterization. This included 36 accessions in each of sorghum, pearl millet, and pigeonpea, conserved at ICRISAT genebank. We genotyped about 15 to 25 individuals within each accession, totaling 1,980 individuals using the DArTSeq approach. This resulted in 45,249, 19,052, and 8,211 high-quality single nucleotide polymorphisms (SNPs) in pearl millet, sorghum, and pigeonpea, respectively. Sorghum had the lowest average phenotypic (0.090) and genotypic (0.135) within accession distances, while pearl millet had the highest average phenotypic (0.227) and genotypic (0.245) distances. Pigeonpea had an average of 0.203 phenotypic and 0.168 genotypic within accession distances. Analysis of molecular variance also confirms the lowest variability within accessions of sorghum (26.3%) and the highest of 80.2% in pearl millet, while an intermediate in pigeonpea (57.0%). The effective sample size required to capture maximum variability and to retain rare alleles while regeneration ranged from 47 to 101 for sorghum, 155 to 203 for pearl millet, and 77 to 89 for pigeonpea accessions. This study will support genebank curators, in understanding the dynamics of population within and among accessions, in devising appropriate germplasm conservation strategies, and aid in their utilization for crop improvement.

Unraveling the Genetic Basis of Key Agronomic Traits of Wrinkled Vining Pea (Pisum sativum L.) for Sustainable Production

“…The DArTseq sequencing method was discovered more than five-fold higher quality SNP markers than GBS. This is due to the higher sequence depth and usage of strict filtering criterion, which the earlier method applied that ultimately lead to generating higher numbers of quality SNPs with less missing data compared to the latter approach ( Allan et al, 2020 ). The SNP markers from two sequencing platforms, however, enumerated the existing genetic diversity similarly.…”

Addressing Iron and Zinc Micronutrient Malnutrition Through Nutrigenomics in Pearl Millet: Advances and Prospects

“…Over singe ( Ape K1) enzyme GbS, two enzyme combinations (SphI and Mlu C1) double digest restriction associated DNA (ddRAD) was found to be superior ( Srivastava et al, 2016 ) and was used to fine map the LG2 drought tolerance QTL ( Srivastava et al, 2017 ). The other genotyping platforms that are available include tunable-GbS (tGbS) ( Ott et al, 2017 ; Liang et al, 2018 ), DArT-seq ( Allan et al, 2020 ); and RNase H2 enzyme-dependent amplicon sequencing (rhAmpSeq) ( Dobosy et al, 2011 ).…”

Genotypic Variation in Cultivated and Wild Sorghum Genotypes in Response to Striga hermonthica Infestation

“…The DArT-seq technology (Sansaloni et al, 2011) that was used to characterize the germplasm proved to be a reliable and cost-effective technology for diversity analysis and confirming hybridity. While there are several studies reporting the use of DArT-seq for diversity analysis in sorghum (Kotla et al, 2019;Allan et al, 2020;Mengistu et al, 2020), this study is the first to use DArT-seq for hybridity testing. The unique SNP markers from this study will be useful for GS and for incorporation into marker panels that aim at the identification of successful hybrids from new crosses involving any of the parents.…”