Identification of main effect and epistatic quantitative trait loci for morphological and yield-related traits in peanut (Arachis hypogaea L.)

Khedikar, Yogendra; Pandey, Manish K.; Sujay, V.; Singh, Sube; Nayak, Spurthi N.; Klein-Gebbinck, H. W.; Cholin, Sarvamangala; Mukri, Ganapati; Garg, Vanika; Upadhyaya, Hari D.; Nadaf, H. L.; Gowda, M. V. C.; Varshney, Rajeev K.; Bhat, Ramesh

doi:10.1007/s11032-017-0764-z

Cited by 16 publications

(20 citation statements)

References 38 publications

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“…The developed data could be utilized in functional genomics research to pin-point targeted candidate genes in groundnut. Trait mapping efforts led to identification of associated genomic regions for several important traits in groundnut including biotic and abiotic stresses, agronomic, yield component and oil quality traits (Agarwal et al, 2018;Khedikar et al, 2018;Pandey et al, 2012Pandey et al, , 2016Pandey et al, , 2017Varshney et al, 2013;Vishwakarma et al, 2017). Most of these studies identified mere loosely associated markers.…”

Section: Discussionmentioning

confidence: 99%

Arachis hypogaea gene expression atlas for fastigiata subspecies of cultivated groundnut to accelerate functional and translational genomics applications

Sinha

Bajaj

Pazhamala

et al. 2020

Plant Biotechnology Journal

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Spatio-temporal and developmental stage-specific transcriptome analysis plays a crucial role in systems biology-based improvement of any species. In this context, we report here the Arachis hypogaea gene expression atlas (AhGEA) for the world's widest cultivated subsp. fastigiata based on RNA-seq data using 20 diverse tissues across five key developmental stages. Approximately 480 million paired-end filtered reads were generated followed by identification of 81 901 transcripts from an early-maturing, high-yielding, drought-tolerant groundnut variety, ICGV 91114. Further, 57 344 genome-wide transcripts were identified with ≥1 FPKM across different tissues and stages. Our in-depth analysis of the global transcriptome sheds light into complex regulatory networks namely gravitropism and photomorphogenesis, seed development, allergens and oil biosynthesis in groundnut. Importantly, interesting insights into molecular basis of seed development and nodulation have immense potential for translational genomics research. We have also identified a set of stable expressing transcripts across the selected tissues, which could be utilized as internal controls in groundnut functional genomics studies. The AhGEA revealed potential transcripts associated with allergens, which upon appropriate validation could be deployed in the coming years to develop consumer-friendly groundnut varieties. Taken together, the AhGEA touches upon various important and key features of cultivated groundnut and provides a reference for further functional, comparative and translational genomics research for various economically important traits.

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Section: Discussionmentioning

confidence: 99%

Arachis hypogaea gene expression atlas for fastigiata subspecies of cultivated groundnut to accelerate functional and translational genomics applications

Sinha

Bajaj

Pazhamala

et al. 2020

Plant Biotechnology Journal

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“…Genetic mapping of peanut yield components has led to the discovery of multiple quantitative trait loci (QTL) for pod and seed size traits including 100_pod_wt, 100_seed_wt, pod length, pod width, seed length, and seed width (Chen et al 2017;Fonceka et al 2012;Hake et al 2017;Khedikar et al 2018;Luo et al 2018;Luo et al 2017;Wang et al 2018). The number of QTL for pod and seed traits ranged from 1 to 92 suggesting that they have a complex genetic architecture.…”

Section: Introductionmentioning

confidence: 99%

Major seed size QTL on chromosome A05 of peanut (Arachis hypogaea) is conserved in the US mini core germplasm collection

et al. 2019

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Pod and seed size are important characteristics for the peanut industry and have been under strong selection pressure since peanut domestication. In order to dissect the genetic control of peanut pod and seed size, a recombinant inbred mapping population from a cross of Florida-07 by GP-NC WS 16 was used to determine the genomic regions associated with traits including 100 pod weight, 100 seed weight, pod weight of double-seeded pods, seed weight of double-seeded pods, and area of double-seeded pods. Nine QTL on linkage groups (LGs) A05, A06, A09, B10, B04, A03, B05, and B08 were associated with pod and seed size. A majority of the QTL have small effects except the locus on LG A05 (93 to 102 Mbp) which explained up to 66% phenotypic variation for all measured pod and seed traits. A comparison of QTL previously reported for yield component traits showed a common QTL on LG A05 was detected in two genetic populations whose parentage is distinct from those used in this study. The markers tightly linked to this major QTL were informative in distinguishing large versus small-seeded germplasm lines in the mini core collection originating from thirty-one countries, suggesting selection for this seed size QTL in large-seeded ecotypes. However, the large seed size allele appeared to co-segregate with a late leaf spot disease susceptibility allele inherited from the Florida-07 parent. Therefore, peanut breeders need to weigh the pros and cons before integrating the large seed size QTL from Florida-07 in their breeding program.

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“…These genotype data together with the phenotype data that are collected from the analyzed accessions were used to perform GWAS analyses for identifying genomic regions that are significantly associated with seven peanut yield-related traits. The identified associated regions were then compared to the QTL loci reported in earlier QTL mapping/GWAS studies (using different sets of peanut accessions comparing to the present study) [6,7,9,12,13,14], and co-localized regions received close examination.…”

Section: Introductionmentioning

confidence: 96%

“…Yield-related traits, such as hundred-seed/pod weight and mature pod number per plant, are mostly quantitative traits, which have been found to be governed by multiple loci and are influenced by environmental factors [5,6]. Understanding the genetic base of yield-related traits is the most important prerequisite for peanut genetic improvement and such understanding has been greatly advanced, especially through approaches that search for quantitative trait loci (QTL).…”

Section: Introductionmentioning

confidence: 99%

“…Understanding the genetic base of yield-related traits is the most important prerequisite for peanut genetic improvement and such understanding has been greatly advanced, especially through approaches that search for quantitative trait loci (QTL). Over the past two decades, QTLs for yield-related traits have been identified mostly by traditional bi-parental QTL mapping [6,7,8,9] and relatively recently by genome-wide association studies (GWAS) [10]. GWAS analysis has some significant advantages over traditional QTL mapping; for example, the much greater historical recombination and genetic diversity that are usually embedded within the studied plant lines for the former significantly increase the mapping resolution of this time-efficient method and make it rather easy for minor effect genes to be detected [11].…”

Section: Introductionmentioning

confidence: 99%

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GWAS Discovery of Candidate Genes for Yield-Related Traits in Peanut and Support from Earlier QTL Mapping Studies

Wang¹,

Cheng²,

et al. 2019

Genes

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Peanut (Arachis hypogaea L.) is one of the most important oil crops worldwide, and its yet increasing market demand may be met by genetic improvement of yield related traits, which may be facilitated by a good understanding of the underlying genetic base of these traits. Here, we have carried out a genome-wide association study (GWAS) with the aim to identify genomic regions and the candidate genes within these regions that may be involved in determining the phenotypic variation at seven yield-related traits in peanut. For the GWAS analyses, 195 peanut accessions were phenotyped and/or genotyped; the latter was done using a genotyping-by-sequencing approach, which produced a total of 13,435 high-quality single nucleotide polymorphisms (SNPs). Analyses of these SNPs show that the analyzed peanut accessions can be approximately grouped into two big groups that, to some extent, agree with the botanical classification of peanut at the subspecies level. By taking this genetic structure as well as the relationships between the analyzed accessions into consideration, our GWAS analyses have identified 93 non-overlapping peak SNPs that are significantly associated with four of the studied traits. Gene annotation of the genome regions surrounding these peak SNPs have found a total of 311 unique candidate genes. Among the 93 yield-related-trait-associated SNP peaks, 12 are found to be co-localized with the quantitative trait loci (QTLs) that were identified by earlier related QTL mapping studies, and these 12 SNP peaks are only related to three traits and are almost all located on chromosomes Arahy.05 and Arahy.16. Gene annotation of these 12 co-localized SNP peaks have found 36 candidates genes, and a close examination of these candidate genes found one very interesting gene (arahy.RI9HIF), the rice homolog of which produces a protein that has been shown to improve rice yield when over-expressed. Further tests of the arahy.RI9HIF gene, as well as other candidate genes especially those within the more confident co-localized genomic regions, may hold the potential for significantly improving peanut yield.

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Identification of main effect and epistatic quantitative trait loci for morphological and yield-related traits in peanut (Arachis hypogaea L.)

Cited by 16 publications

References 38 publications

Arachis hypogaea gene expression atlas for fastigiata subspecies of cultivated groundnut to accelerate functional and translational genomics applications

Arachis hypogaea gene expression atlas for fastigiata subspecies of cultivated groundnut to accelerate functional and translational genomics applications

Major seed size QTL on chromosome A05 of peanut (Arachis hypogaea) is conserved in the US mini core germplasm collection

GWAS Discovery of Candidate Genes for Yield-Related Traits in Peanut and Support from Earlier QTL Mapping Studies

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