Haplotype Networking of GWAS Hits for Citrulline Variation Associated with the Domestication of Watermelon.

Joshi Joshi,Reddy Reddy,Nimmakayala Nimmakayala,Shinde Shinde,Levi Levi,Lopez-Ortiz Lopez-Ortiz,Panicker Panicker,Alaparthi Alaparthi,Abburi Abburi

doi:10.3390/ijms20215392

Abstract

Watermelon is a good source of citrulline, a non-protein amino acid. Citrulline has several therapeutic and clinical implications as it produces nitric oxide via arginine. In plants, citrulline plays a pivotal role in nitrogen transport and osmoprotection. The purpose of this study was to identify single nucleotide polymorphism (SNP) markers associated with citrulline metabolism using a genome-wide association study (GWAS) and understand the role of citrulline in watermelon domestication. A watermelon collection consisting of 187 wild, landraces, and cultivated accessions was used to estimate citrulline content. An association analysis involved a total of 12,125 SNPs with a minor allele frequency (MAF)>0.05 in understanding the population structure and phylogeny in light of citrulline accumulation. Wild egusi types and landraces contained low to medium citrulline content, whereas cultivars had higher content, which suggests that obtaining higher content of citrulline is a domesticated trait. GWAS analysis identified candidate genes (ferrochelatase and acetolactate synthase) showing a significant association of SNPs with citrulline content. Haplotype networking indicated positive selection from wild to domesticated watermelon. To our knowledge, this is the first study showing genetic regulation of citrulline variation in plants by using a GWAS strategy. These results provide new insights into the citrulline metabolism in plants and the possibility of incorporating high citrulline as a trait in watermelon breeding programs.

Highlights

Non-protein amino acids present in legumes, fruits, seeds, and nuts are ubiquitous in the human diet
The current study examined the collection of 144 Citrullus. lanatus var. vulgaris accessions, 34 semi-wild types, and 9 accessions belonging to Citrullus
Primitive dessert watermelon landraces, with naturally low sugar content, were expected to be valuable sources of bioactive compounds [41], our study demonstrates that citrulline content is, in general, lower in landraces and egusi types

Summary

Introduction

Non-protein amino acids present in legumes, fruits, seeds, and nuts are ubiquitous in the human diet. Besides containing several health-promoting bioactive compounds, fruits accumulate substantial amounts of free non-protein amino acids. Vulgaris) fruits accumulate a substantial amount of a non-protein amino acid—citrulline. Members of the Cucurbitaceae family are generally considered to contain relatively large amounts of free citrulline, watermelon accumulates the highest quantities [13]. Citrulline content in watermelons is spatially and developmentally regulated, with the highest values occurring at fruit maturity [14,15,16,17,18]. Several studies reported the presence of genotypic variation for citrulline content in a selected set of cultivated watermelon varieties [11,16,18,20,21]. A moderate to high range of heritability [21,22] for citrulline content within cultivated watermelons implies its possible genetic improvement with selective breeding

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