Genotyping-by-Sequencing Derived Genetic Linkage Map and Quantitative Trait Loci for Sugar Content in Onion (Allium cepa L.)

Abstract

Onion (2n = 2x = 16) has been a nutritional, medicinal and economically valuable vegetable crop all over the world since ancient times. To accelerate the molecular breeding in onion, genetic linkage maps are prerequisite. However, construction of genetic linkage maps of onion remains relatively rudimentary due to a large genome (about 16.3 Gbp) as well as biennial life cycle, cross-pollinated nature, and high inbreeding depression. In this study, we constructed single nucleotide polymorphism (SNP)-based genetic linkage map of onion in an F2 segregating population derived from a cross between the doubled haploid line ‘16P118′ and inbred line ‘Sweet Green’ through genotyping by sequencing (GBS). A total of 207.3 Gbp of raw sequences were generated using an Illumina HiSeq X system, and 24,341 SNPs were identified with the criteria based on three minimum depths, lower than 30% missing rate, and more than 5% minor allele frequency. As a result, an onion genetic linkage map consisting of 216 GBS-based SNPs were constructed comprising eight linkage groups spanning a genetic length of 827.0 cM. Furthermore, we identified the quantitative trait loci (QTLs) for the sucrose, glucose, fructose, and total sugar content across the onion genome. We identified a total of four QTLs associated with sucrose (qSC4.1), glucose (qGC5.1), fructose (qFC5.1), and total sugar content (qTSC5.1) explaining the phenotypic variation (R2%) ranging from 6.07–11.47%. This map and QTL information will contribute to develop the molecular markers to breed the cultivars with high sugar content in onion.

Genetic resources and breeding of maize for Striga resistance: a review

“…Genotyping by sequencing (GBS) ( De Donato et al., 2013 ), restriction-associated DNA (RAD), complexity reduction of polymorphic sequences (CRoPS) ( van Orsouw et al., 2007 ), and diversity arrays technology (DArT) are among available approaches to do SNPs discovering and genotyping. However, GBS is the most popular approach to the identification of SNPs in plants ( Negro et al., 2019 ; Heinrich et al., 2020 ; Lee et al., 2021 ). The GBS is a novel application of NGS protocols for discovering and genotyping SNPs in crop genomes and populations.…”

Turning Garlic into a Modern Crop: State of the Art and Perspectives

“…Genotyping a large number of molecular markers in all individuals of a population can be achieved though techniques, such as genotyping by sequencing (GBS) [ 56 ] or restriction-site-associated DNA (RAD) sequencing (RAD-Seq) [ 57 ], and is a crucial preliminary step for mapping and identifying genes and QTLs relevant for crop breeding. Despite the significant challenge posed by the large size of the garlic genome, GBS methods have been successfully applied to construct at least three linkage maps in closely related species, such as onion [ 58 , 59 , 60 ]. The first of these maps was made using 96 F 2 plants from a cross involving 2 different onion cultivars, which contained more than 10,000 single-nucleotide polymorphisms (SNPs) spanning the 8 chromosomes of the onion haploid genome [ 58 ].…”

CRISPR/Cas9-mediated editing of PHYTOENE DESATURASE gene in onion (Allium cepa L.)

“…Since domestication, productivity, quality, and resilience to biotic and abiotic stresses have been improved in onions using several conventional breeding practices. However, conventional approaches have not produced substantial progress in the genetic improvement of onions and have been hampered by the biennial life cycle, cross-pollinated nature, and severe inbreeding depression ( McCallum, 2007 ; Sudha et al., 2019 ; Lee et al., 2021 ). Despite the fact that onions have a large genetic variability, crop improvement has lagged behind other monocot crops ( McCallum, 2007 ; Varshney et al., 2012 ).…”