A high-density genetic map constructed using specific length amplified fragment (SLAF) sequencing and QTL mapping of seed-related traits in sesame (Sesamum indicum L.)

Abstract

BackgroundSesame (Sesamum indicum L., 2n = 2x = 26) is an important oilseed crop with high oil content but small seed size. To reveal the genetic loci of the quantitative seed-related traits, we constructed a high-density single nucleotide polymorphism (SNP) linkage map of an F2 population by using specific length amplified fragment (SLAF) technique and determined the quantitative trait loci (QTLs) of seed-related traits for sesame based on the phenotypes of F3 progeny.ResultsThe genetic map comprised 2159 SNP markers distributed on 13 linkage groups (LGs) and was 2128.51 cM in length, with an average distance of 0.99 cM between adjacent markers. QTL mapping revealed 19 major-effect QTLs with the phenotypic effect (R2) more than 10%, i.e., eight QTLs for seed coat color, nine QTLs for seed size, and two QTLs for 1000-seed weight (TSW), using composite interval mapping method. Particularly, LG04 and LG11 contained collocated QTL regions for the seed coat color and seed size traits, respectively, based on their close or identical locations. In total, 155 candidate genes for seed coat color, 22 for seed size traits, and 54 for TSW were screened and analyzed.ConclusionsThis report presents the first QTL mapping of seed-related traits in sesame using an F2 population. The results reveal the location of specific markers associated with seed-related traits in sesame and provide the basis for further seed quality traits research.

Genome-wide association uncovers the genetic architecture of tradeoff between flowering date and yield components in sesame

“…Seed size (TSW) is known to have moderatehigh heritability in sesame (Uzun et al, 2013;Kalaiyarasi et al, 2019), as was found in the current study (0.88) and other crops, such as wheat (Sukumaran et al, 2018) and pea (Pisum sativum L.; Huang et al, 2017), was associated with only one region in 2020, with no overlap with SNPP and SYPP. Likewise, a small number of associated loci for TSW were found in bi-parental sesame populations (Du et al, 2019;Teboul et al, 2020), which may suggest that this trait is under less complex genetic control or under the regulation of many small-effect genomic regions. The absence of significant genomic signs for TSW (as well as other traits in the current study) indicates that other approaches, such as genomic prediction (Crossa et al, 2017), may contribute to understanding its genetic basis.…”

Transcriptome Dynamics during Black and White Sesame (Sesamum indicum L.) Seed Development and Identification of Candidate Genes Associated with Black Pigmentation

“…Flavonoids represent the main secondary metabolites that influence plant seed coat color [ 46 ]. Du et al [ 28 ] mapped 14 QTL and uncovered 155 candidate genes for sesame seed coat color that were enriched principally in two pathways, diterpenoid biosynthesis and oxidative phosphorylation. Other studies in sesame detected that two major genes with additive-dominant-epistatic effects plus polygenes with additive-dominant-epistatic effects control the seed coat color, and several other major QTL have been identified [ 25 , 27 ].…”

“…The gene SIN_1016759/PPO had been reported as the candidate gene for black seed coat development in sesame [ 24 , 26 ]. It was also included in the list of sesame seed coat candidate genes reported recently by Du et al [ 28 ]. In plants, browning reactions on seed coat pigments are often induced by the oxidation of phenolic compounds by polyphenol oxidases (PPO) such as laccases and tyrosinases and result in melanin formation mostly [ 53 , 54 ].…”

“…Zhang et al [ 27 ] have detected four QTL (QTL1-1, QTL11-1, QTL11-2, and QTL13-1) for seed coat color, whereas Wang et al [ 25 ] have detected nine QTL (qSCa-8.2, qSCb-4.1, qSCb-8.1, qSCb-11.1, qSCl-4.1, qSCl-8.1, qSCl-11.1, qSCa-4.1, and qSCa-8.1) located on chr4, chr8, and chr11. Recently, by using the composite interval mapping method, Du et al [ 28 ] uncovered eight major-effect QTL for sesame seed coat color on chromosomes 4, 9, and 12. Moreover, they screened the QTL locations and identified 155 candidate genes associated with sesame seed coat color.…”

Genome-Wide Discovery of InDel Markers in Sesame (Sesamum indicum L.) Using ddRADSeq

“…A few mapping and marker-assisted selection studies have also been conducted with the use of AFLP markers for the closed capsule mutant trait [ 26 ]; RAPD markers for corolla color [ 27 ]; and SSR markers for determinate growth habit [ 12 ], male-sterile gene [ 28 ], and oil and protein content [ 2 ] to improve the efficiency of sesame breeding programs. A large number of single nucleotide polymorphisms (SNPs) have also been identified with the advent of next-generation sequencing technology and have been used for the exploitation of genetic diversity [ 29 , 30 ], the construction of high-density linkage mapping [ 31 , 32 , 33 ], and the identification of candidate genes for the improvement of sesame production [ 34 , 35 , 36 , 37 ].…”