Dataset Information

Genome-Wide Association Studies of 39 Seed Yield-Related Traits in Sesame (Sesamum indicum L.).

ABSTRACT: Sesame is poised to become a major oilseed crop owing to its high oil quality and adaptation to various ecological areas. However, the seed yield of sesame is very low and the underlying genetic basis is still elusive. Here, we performed genome-wide association studies of 39 seed yield-related traits categorized into five major trait groups, in three different environments, using 705 diverse lines. Extensive variation was observed for the traits with capsule size, capsule number and seed size-related traits, found to be highly correlated with seed yield indexes. In total, 646 loci were significantly associated with the 39 traits (p < 10^-7) and resolved to 547 quantitative trait loci QTLs. We identified six multi-environment QTLs and 76 pleiotropic QTLs associated with two to five different traits. By analyzing the candidate genes for the assayed traits, we retrieved 48 potential genes containing significant functional loci. Several homologs of these candidate genes in Arabidopsis are described to be involved in seed or biomass formation. However, we also identified novel candidate genes, such as SiLPT3 and SiACS8, which may control capsule length and capsule number traits. Altogether, we provided the highly-anticipated basis for research on genetics and functional genomics towards seed yield improvement in sesame.

SUBMITTER: Zhou R

PROVIDER: S-EPMC6164633 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature

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Genome-Wide Association Studies of 39 Seed Yield-Related Traits in Sesame (<i>Sesamum indicum</i> L.).

Zhou Rong R Dossa Komivi K Li Donghua D Yu Jingyin J You Jun J Wei Xin X Zhang Xiurong X

International journal of molecular sciences 20180917 9

Sesame is poised to become a major oilseed crop owing to its high oil quality and adaptation to various ecological areas. However, the seed yield of sesame is very low and the underlying genetic basis is still elusive. Here, we performed genome-wide association studies of 39 seed yield-related traits categorized into five major trait groups, in three different environments, using 705 diverse lines. Extensive variation was observed for the traits with capsule size, capsule number and seed size-re ...[more]

PMID: 30227628

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Project description:To enhance sesame yield, it is important to utilize diverse parents in breeding programs and implement an effective selection procedure, which exploits the association of quantitative traits. Therefore, the objective of this experiment was to explore the correlation among quantitative traits and assess genetic variability and diversity using both qualitative and quantitative traits. Correlation coefficients indicated a noteworthy (P < 0.001) positive phenotypic (rp) and genotypic (rg) correlation between seed yield and various traits: plant height (rp = 0.60; rg = 0.58), length of the capsule-bearing zone (rp = 0.77; rg = 0.80), number of capsules on the main stem (rp = 0.80; rg = 0.85), primary branches (rp = 0.66; rg = 0.66), and capsules per plant (rp = 0.90; rg = 0.91). In contrast, a negative correlation (P < 0.001) was observed between yield and bacterial blight disease severity, both phenotypically (rp = -0.60) and genotypically (rg = -0.76). The analysis of path coefficients indicated that the most substantial positive direct effect on yield (0.77) was attributed to capsules per plant, whereas other traits associated with yield exhibited a significant indirect influence on yield through capsules per plant. Qualitative traits exhibited diversity, except for plant growth type, plant growth habit, and stem branching. Shannon-Weaner (H) and Simpson (1-D) diversity indices were higher for interior corolla color (H = 1.63; 1-D = 0.66), seed color (H = 1.50; 1-D = 0.46), and capsule beak type (H = 1.08; 1-D = 0.50). The analysis of variance indicated a notable variation among the examined genotypes regarding quantitative traits, excluding internode length. The plant materials were divided into five clusters through cluster analysis, where clusters I to V consisted of 21, 29, 4, 4, and 6 genotypes, respectively. The current study has shown that the yield of sesame can be enhanced through indirect selection for traits associated with yield, particularly the highest number of capsules per plant. Furthermore, examinations of genetic diversity confirmed the presence of variability within the assessed genotypes, providing valuable insights for upcoming sesame breeding programs.

Project description:Sesame is predominantly cultivated in rainfed and low fertile lands and is frequently exposed to terminal drought. Sesamum species inhabiting dryland ecosystems adaptively diverge from those inhabiting rainfed habitats, and drought-specific traits have a genetic basis. In sesame, traits associated with drought conditions have not been explored to date, yet studies of these traits are needed given that drought is predicted to become more frequent and severe in many parts of the world because of climate change. Here, 76 accessions from the available Indian core set were used to quantify variation in several traits under irrigated (WW) and terminal drought stress (WS) conditions as well as their association with seed yield over two consecutive years. The range of trait variation among the studied genotypes under WW and WS was significant. Furthermore, the traits associated with seed yield under WW and WS differed. The per se performance of the accessions indicated that the expression of most traits was reduced under WS. The correlation analysis revealed that the number of branches, leaf area (LA), leaves dry weight (LDW), number of capsules plant-1, and harvest index (HI) were positively correlated with seed yield under WW and WS, and total dry matter (TDM), plant stem weight, and canopy temperature (CT) were negatively correlated with seed yield under WW and WS, indicating that smaller and cooler canopy genotypes had higher yields. The genotypes IC-131936, IC-204045, IC-204861, IC-205363, IC-205311, and IC-73576 with the highest seed yields were characterized by low canopy temperature, high relative water content, and high harvest index under WS. Phenotypic and molecular diversity analysis was conducted on genotypes along with checks. Phenotypic diversity was assessed using multivariate analysis, whereas molecular diversity was estimated using simple sequence repeat (SSR) loci to facilitate the use of sesame in breeding and genetic mapping. SSRs showed low allelic variation, as indicated by a low average number of alleles (2.31) per locus, gene diversity (0.25), and polymorphism information content (0.22). Cluster analysis (CA) [neighbor-joining (NJ) tree] revealed three major genotypic groups and structure analysis showed 4 populations. The diverse genotypes identified with promising morpho-physiological traits can be used in breeding programs to develop new varieties.

Project description:BackgroundSesame (Sesamum indicum L., 2n = 26) is an important oilseed crop with an estimated genome size of 369 Mb. The genetic basis, including the number and locations of quantitative trait loci (QTLs) of sesame grain yield and quality remain poorly understood, due in part to the lack of reliable markers and genetic maps. Here we report on the construction of a hitherto most high-density genetic map of sesame using the restriction-site associated DNA sequencing (RAD-seq) combined with 89 PCR markers, and the identification of grain yield-related QTLs using a recombinant inbred line (RIL) population.ResultIn total, 3,769 single-nucleotide polymorphism (SNP) markers were identified from RAD-seq, and 89 polymorphic PCR markers were identified including 44 expressed sequence tag-simple sequence repeats (EST-SSRs), 10 genomic-SSRs and 35 Insertion-Deletion markers (InDels). The final map included 1,230 markers distributed on 14 linkage groups (LGs) and was 844.46 cM in length with an average of 0.69 cM between adjacent markers. Using this map and RIL population, we detected 13 QTLs on 7 LGs and 17 QTLs on 10 LGs for seven grain yield-related traits by the multiple interval mapping (MIM) and the mixed linear composite interval mapping (MCIM), respectively. Three major QTLs had been identified using MIM with R2 > 10.0% or MCIM with ha 2 > 5.0%. Two co-localized QTL groups were identified that partially explained the correlations among five yield-related traits.ConclusionThree thousand eight hundred and four pairs of new DNA markers including SNPs and InDels were developed by RAD-seq, and a so far most high-density genetic map was constructed based on these markers in combination with SSR markers. Several grain yield-related QTLs had been identified using this population and genetic map. We report here the first QTL mapping of yield-related traits with a high-density genetic map using a RIL population in sesame. Results of this study solidified the basis for studying important agricultural traits and implementing marker-assisted selection (MAS) toward genetic improvement in sesame.

Dataset Information

Genome-Wide Association Studies of 39 Seed Yield-Related Traits in Sesame (Sesamum indicum L.).

Publications

Genome-Wide Association Studies of 39 Seed Yield-Related Traits in Sesame (<i>Sesamum indicum</i> L.).

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