Development and Application of High‐Density Axiom Cajanus SNP Array with 56K SNPs to Understand the Genome Architecture of Released Cultivars and Founder Genotypes

Abstract

Core Ideas Axiom Cajanus SNP array revealed genetic architecture and temporal diversity in pigeonpea varieties. As one of the major outputs of next‐generation sequencing (NGS), a large number of genome‐wide single‐nucleotide polymorphisms (SNPs) have been developed in pigeonpea [Cajanus cajan (L.) Huth.]. However, SNPs require a genotyping platform or assay to be used in different evolutionary studies or in crop improvement programs. Therefore, we developed an Axiom Cajanus SNP array with 56K SNPs uniformly distributed across the genome and assessed its utility in a genetic diversity study. From the whole‐genome resequencing (WGRS) data on 104 pigeonpea lines, ∼2 million sequence variations (SNPs and insertion–deletions [InDels]) were identified, from which a subset of 56,512 unique and informative sequence variations were selected to develop the array. The Axiom Cajanus SNP array developed was used for genotyping 103 pigeonpea lines encompassing 63 cultivars released between 1960 and 2014 and 40 breeding, germplasm, and founder lines. Genotyping data thus generated on 103 pigeonpea lines provided 51,201 polymorphic SNPs and InDels. Genetic diversity analysis provided in‐depth insights into the genetic architecture and trends in temporal diversity in pigeonpea cultivars. Therefore, the continuous use of the high‐density Axiom Cajanus SNP array developed will accelerate high‐resolution trait mapping, marker‐assisted breeding, and genomic selection efforts in pigeonpea.

A 62K genic-SNP chip array for genetic studies and breeding applications in pigeonpea (Cajanus cajan L. Millsp.)

“…A major limitation in genetic dissection of complex traits in pigeonpea has been the unavailability of high-density genotyping assays that can be utilized effectively for the genetic improvement of the crop 22 . Hence, we used the improved second draft of the pigeonpea genome 26 , and re-sequencing data of 45 diverse pigeonpea varieties to develop a largely SC genes based 62 K Axiom genic-SNP chip for this purpose.…”

“…Several medium-density arrays have been developed for genetic analysis and breeding applications in rice [6][7][8][9][10] . Similarly, high-density chip arrays have been developed for rice [11][12][13][14] , sunflower 15 , soybean 16 , oil palm 17 , maize 18,19 , wheat 20,21 and pigeonpea 22 as well as animal species including chicken 23 , cattle 24 and human 25 . However, all these arrays incorporate genome wide mostly intergenic SNPs and single SNP per locus, except for the 50 K genic-SNP chip of rice which is based on single-copy (SC) genes 14 .…”

“…However, all these arrays incorporate genome wide mostly intergenic SNPs and single SNP per locus, except for the 50 K genic-SNP chip of rice which is based on single-copy (SC) genes 14 . The available pigeonpea SNP array by Saxena et al (2018) is also based largely (70.53%) on intergenic regions of the genome. Only 5166 of the total 56,512 SNPs in this chip belong to exonic regions 22 .…”

“…The available pigeonpea SNP array by Saxena et al (2018) is also based largely (70.53%) on intergenic regions of the genome. Only 5166 of the total 56,512 SNPs in this chip belong to exonic regions 22 . The SC genes based SNP array of rice has proven efficient for studying evolutionary relationships, haplotype analysis and QTL mapping of complex traits in rice 14 .…”

Nested‐association mapping (NAM)‐based genetic dissection uncovers candidate genes for seed and pod weights in peanut (Arachis hypogaea)

“…Reference genome sequences of both wild diploid progenitors A. ipaensis and A. duranensis (Bertioli et al , ; Chen et al , ; Lu et al , ), as well as allotetraploid cultivated peanut A. hypogaea (Bertioli et al , ; Chen et al , ; Zhuang et al , ), have recently been assembled by the international peanut community and are important resources for sequence‐based trait mapping and candidate gene discovery. This has also facilitated the development of high‐resolution SNP arrays in peanut (Clevenger et al , ; Pandey et al , ), which have shown great utility in fine trait mapping in other crops such as rice (Thomson et al , ), soybean (Xavier et al , ), maize (Yan et al , ), wheat (Wang et al , ), chickpea (Roorkiwal et al , ) and pigeonpea (Saxena et al , ; Yadav et al , ).…”