Pod and seed trait QTL identification to assist breeding for peanut market preferences

Chavarro, Carolina; Chu, Ye; Holbrook, C. Corley; Isleib, T. G.; Bertioli, David J.; Hovav, Ran; Butts, Christopher L.; Lamb, Marshall C.; Sorensen, Ronald B.; Jackson, Scott A.; Ozias‐Akins, Peggy

doi:10.1101/738914

Cited by 3 publications

(2 citation statements)

References 81 publications

(15 reference statements)

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“…Pod-related traits (PRTs) are important agronomic traits not only influencing peanut yield, but also affecting pod appearance and processing quality. Although many QTLs underlying PRTs were identified through natural populations [30][31][32][33][34][35], more information was still needed for elucidating the genetic mechanism underlying these traits. EMS-induced mutagenesis is a suitable choice to supplement the study in the natural population.…”

Section: Discussionmentioning

confidence: 99%

Construction of EMS-Induced Peanut Mutant Libraries and Identification of Pod-Related Traits Mutant Lines

Chen¹,

Xiong²,

Xu³

et al. 2023

Phyton

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Peanut (Arachis hypogaea L.) is an oil and economic crop of vital importance, and peanut pod is the key organ influencing the yield and processing quality. Hence, the Pod-related traits (PRTs) are considered as important agronomic traits in peanut breeding. To broaden the variability of PRTs in current peanut germplasms, three elite peanut cultivars were used to construct Ethyl methane sulfonate (EMS)-induced mutant libraries in this study. The optimal EMS treatment conditions for the three peanut varieties were determined. It was found that the median lethal dose (LD50) of EMS treatment varied greatly among different genotypes. Finally, the EMS-induced peanut mutant libraries were constructed and a total of 124 mutant lines for PRTs were identified and evaluated. Furthermore, "M-8070", one of the mutant lines for pod constriction, was re-sequenced via high-throughput sequencing technology. The genome-wide variations between "M-8070" and its wild parent "Fuhua 8" (FH 8) were detected. 2994 EMS-induced single nucleotide polymorphisms (SNPs) and 1188 insertion-deletions (InDels) between "M-8070" and its wild parent were identified. The predominant SNP mutation type was C/G to T/A transitions, while the predominant InDel mutation type was "1-bp". We analyzed the distribution of identified mutations and annotated their functions. Most of the mutations (91.68% of the SNPs and 77.69% of the InDels) were located in the intergenic region. 72 SNPs were identified in the exonic region, leading to 27 synonymous, 43 nonsynonymous and 2 stop-gain variation for gene structure. 13 Indels were identified in the exonic region, leading to 4 frame-shift, 8 non-frame-shift and 1 stop-gain variations of genes. These mutations may lead to the phenotypic variation of "M-8070". Our study provided valuable resources for peanut improvement and functional genomic research.

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Section: Discussionmentioning

confidence: 99%

Construction of EMS-Induced Peanut Mutant Libraries and Identification of Pod-Related Traits Mutant Lines

Chen¹,

Xiong²,

Xu³

et al. 2023

Phyton

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“…Each individual plant that entered the QTL validation experiment was genotyped by two KASPar markers designed from the QTL regions conditioning stem rot resistance, that is, KASPar marker A01_4 and A05_1 (Supplemental Table S2). Although the A01 QTL region spanned 65 Mbp, it was located in the pericentromeric region and minimum recombination was found within the population (Chavarro et al, 2019). Therefore, one KASPar marker (A01_4) was designed based on the highest dSNP between the bulks to facilitate the genotyping of the NC subpopulation.…”

Section: Genotypingmentioning

confidence: 99%

Quantitative trait loci sequencing–derived molecular markers for selection of stem rot resistance in peanut

Cui

Clevenger²,

Chu

et al. 2020

Crop Science

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Developing markers linked to key traits has been a focus of peanut (Arachis hypogaea L.) genomics in the postgenome era. Multiple disease resistance traits have been found to be qualitative and controlled by major quantitative trait loci (QTL) or even single genes while others are more complex. Southern stem rot (stem rot in short) is a devastating disease of peanut caused by the fungus Sclerotium rolfsii. It has been one of the most damaging diseases of peanut with regard to both cost of control and yield loss in the southeastern United States for the last decade. The disease is initiated annually from sclerotia in the soil. The nonuniform distribution of these propagules leads to the nonuniform development of disease, which makes phenotyping and genetic mapping of resistance difficult. Here we report the mapping of two QTL regions controlling stem rot resistance in peanut. Using careful field evaluation, resistant and susceptible bulks were identified from a recombinant inbred line (RIL) population and subjected to QTL sequencing (QTL‐seq). Developed SNP markers linked to the QTL were validated in a blind selection test by selecting only with markers in a part of the population not used for initial analysis. The lines selected for bulk sequencing also were shown to have strong separation for resistance in an independent field experiment. This work not only delivers markers for marker‐assisted selection (MAS) for an important disease in peanut but shows that QTL‐seq can work effectively even when considering highly complex, and quantitative traits.

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Insights into the Genomic Architecture of Seed and Pod Quality Traits in the U.S. Peanut Mini-Core Diversity Panel

Patel

Wang²,

Dang

et al. 2022

Plants

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Traits such as seed weight, shelling percent, percent sound mature kernels, and seed dormancy determines the quality of peanut seed. Few QTL (quantitative trait loci) studies using biparental mapping populations have identified QTL for seed dormancy and seed grade traits. Here, we report a genome-wide association study (GWAS) to detect marker–trait associations for seed germination, dormancy, and seed grading traits in peanut. A total of 120 accessions from the U.S. peanut mini-core collection were evaluated for seed quality traits and genotyped using Axiom SNP (single nucleotide polymorphism) array for peanut. We observed significant variation in seed quality traits in different accessions and different botanical varieties. Through GWAS, we were able to identify multiple regions associated with sound mature kernels, seed weight, shelling percent, seed germination, and dormancy. Some of the genomic regions that were SNP associated with these traits aligned with previously known QTLs. For instance, QTL for seed dormancy has been reported on chromosome A05, and we also found SNP on the same chromosome associated with seed dormancy, explaining around 20% of phenotypic variation. In addition, we found novel genomic regions associated with seed grading, seed germination, and dormancy traits. SNP markers associated with seed quality and dormancy identified here can accelerate the selection process. Further, exploring the function of candidate genes identified in the vicinity of the associated marker will assist in understanding the complex genetic network that governs seed quality.

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Pod and seed trait QTL identification to assist breeding for peanut market preferences

Cited by 3 publications

References 81 publications

Construction of EMS-Induced Peanut Mutant Libraries and Identification of Pod-Related Traits Mutant Lines

Construction of EMS-Induced Peanut Mutant Libraries and Identification of Pod-Related Traits Mutant Lines

Quantitative trait loci sequencing–derived molecular markers for selection of stem rot resistance in peanut

Insights into the Genomic Architecture of Seed and Pod Quality Traits in the U.S. Peanut Mini-Core Diversity Panel

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