Discovery of genome-wide genetic variations and development of first set of InDel markers for genetics research in cashew

Abstract

Cashew nut is an edible tree nut having great industrial applications. Cashew and its products (nut shell liquid and kernel oil) are used in various food preparations, medicines, green energy feedstocks and polymer synthesis making it an industrially important tree. In spite of great economic importance, genetics and molecular studies in cashew are lagging due to a largely unexplored genome and scarcity of robust genome-wide molecular markers. Here, we resequenced the whole genome of Nethra Vaman, a commercial clone of cashew, and identified and characterized their genome-wide variants (GVs): 420,560 SNPs and 26,987 InDels by aligning with the reported draft genome of cashew cv. Bhaskara. The mean density of SNPs was 2,867.78 per Mb of the genome while the mean density of InDels was 184.02 per Mb. KEGG pathway analysis of the genes with GVs revealed that apart from the primary metabolic pathways, plant hormone signal transduction and Mitogen-activated protein kinase (MAPK) pathways were enriched. Besides, the first set of InDel markers (88) possessing advantages of both SSR and SNP markers was developed, and 87.5% of them were highly informative (PIC value ≥0.50). The PIC value of InDel markers ranged from 0.11 (AoINDL-16) to 0.85 (AoINDL-1) with a mean of 0.66. Cross-species amplification of InDel markers showed 84.68%, 79.84%, 74.19%, and 58.06% successful amplification in A. othonianum, A. microcarpum, A. pumilum and S. anacardium, respectively. Genetic diversity analysis using 14 informative InDel markers by UPGMA method clustered the 64 accessions into three main clusters and a total of 200 alleles were identified with a mean of 14.29. AMOVA analysis showed that 6% of genetic variations were attributable to among populations while 94% was attributable to individuals within and among populations. Further, InDel markers were assayed for hybridity ascertaining in A. occidentale × A. microcarpum progeny and the hybrid purity index of markers varied from 45.45 % (AoINDL-40) to 94.5% (AoINDL-77). Thus, the genomic resources, identification and annotation of GVs, and the new class of markers designed here will be valuable for molecular biology, genetics, and molecular breeding in cashew and related Anacardium species.