Identification of QTL for kernel weight and size and analysis of the pentatricopeptide repeat (PPR) gene family in cultivated peanut (Arachis hypogaea L.)

Fang, Yuanjin; Liu, Hua; Qin, Li; Qi, Feiyan; Sun, Ziqi; Wu, Jihua; Dong, Wenzhao; Huang, Bingyan; Zhang, Xinyou

doi:10.1186/s12864-023-09568-y

Cited by 2 publications

(1 citation statement)

References 45 publications

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“…The linkage drag of desirable and undesirable traits often imposes biological constraints in developing improved cultivars by conventional crossing and selection [6]. The crucial factors that affect the yield are the 100-pod weight (HPW), 100-seed weight (HSW), haulm yield, and shelling percentage (SP) [7]. Traditional breeding methods face challenges when dealing with these quantitative traits.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Mapping of Quantitative Trait Loci for Yield-Attributing Traits of Peanut

Joshi,

Soni,

Sharma

et al. 2024

Genes

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Peanuts (Arachis hypogaea L.) are important high-protein and oil-containing legume crops adapted to arid to semi-arid regions. The yield and quality of peanuts are complex quantitative traits that show high environmental influence. In this study, a recombinant inbred line population (RIL) (Valencia-C × JUG-03) was developed and phenotyped for nine traits under two environments. A genetic map was constructed using 1323 SNP markers spanning a map distance of 2003.13 cM. Quantitative trait loci (QTL) analysis using this genetic map and phenotyping data identified seventeen QTLs for nine traits. Intriguingly, a total of four QTLs, two each for 100-seed weight (HSW) and shelling percentage (SP), showed major and consistent effects, explaining 10.98% to 14.65% phenotypic variation. The major QTLs for HSW and SP harbored genes associated with seed and pod development such as the seed maturation protein-encoding gene, serine-threonine phosphatase gene, TIR-NBS-LRR gene, protein kinase superfamily gene, bHLH transcription factor-encoding gene, isopentyl transferase gene, ethylene-responsive transcription factor-encoding gene and cytochrome P450 superfamily gene. Additionally, the identification of 76 major epistatic QTLs, with PVE ranging from 11.63% to 72.61%, highlighted their significant role in determining the yield- and quality-related traits. The significant G × E interaction revealed the existence of the major role of the environment in determining the phenotype of yield-attributing traits. Notably, the seed maturation protein-coding gene in the vicinity of major QTLs for HSW can be further investigated to develop a diagnostic marker for HSW in peanut breeding. This study provides understanding of the genetic factor governing peanut traits and valuable insights for future breeding efforts aimed at improving yield and quality.

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Section: Introductionmentioning

confidence: 99%

Genome-Wide Mapping of Quantitative Trait Loci for Yield-Attributing Traits of Peanut

Joshi,

Soni,

Sharma

et al. 2024

Genes

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Co-localization of quantitative trait loci for pod and kernel traits and development of molecular marker for kernel weight on chromosome Arahy05 in peanut (Arachis hypogaea L.)

Fang,

Liu,

Sun

et al. 2024

Theor Appl Genet

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Key message Stable QTL for pod and kernel traits were co-localized on chromosome Arahy05, and an INDEL marker at 106,411,957 on Arahy05 was developed and validated to be useful for marker-assisted selection of kernel weight. Abstract Pod and kernel traits, such as hundred pod weight (HPW), and hundred kernel weight (HKW), along with pod and kernel sizes, are pivotal determinants of yield in peanut breeding programs. This study sought to identify quantitative trait loci (QTL) that are associated with these pod and kernel traits in peanuts. To achieve this, a recombinant inbred line (RIL) population, was derived from a cross between Yuhua15, a cultivar known for its high yield, and a germplasm accession W1202. The investigation uncovered stable and major QTL that are significantly associated with both pod and kernel weight and were consistently co-localized on chromosomes Arahy05 and Arahy08. Furthermore, an INDEL marker was identified and characterized in the QTL interval on Arahy05. An extensive re-sequencing analysis comprising 395 germplasm accessions led to the discovery of two principal haplotypes within a 500-kb window flanking the aforementioned INDEL marker. The haplotypes exhibited a significant correlation with the HKW in our diverse panel of germplasm accessions. Notably, the 170 accessions harboring the haplotype associated with an increased HKW primarily represented botanical varieties, specifically Arachis hypogaea var. hypogaea and A. hypogaea var. hirsuta . On the other hand, the 137 accessions associated with the alternative haplotype, which corresponded to a reduced HKW, were predominately identified as belonging to botanical varieties within A. hypogaea subsp. fastigiata . The INDEL marker located on Arahy05, which demonstrates close linkage to the pod and kernel traits, would be an efficient approach for marker-assisted selection (MAS) of pod and kernel weight in breeding programs. Supplementary Information The online version contains supplementary material available at 10.1007/s00122-024-04749-z.

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Identification of QTL for kernel weight and size and analysis of the pentatricopeptide repeat (PPR) gene family in cultivated peanut (Arachis hypogaea L.)

Cited by 2 publications

References 45 publications

Genome-Wide Mapping of Quantitative Trait Loci for Yield-Attributing Traits of Peanut

Genome-Wide Mapping of Quantitative Trait Loci for Yield-Attributing Traits of Peanut

Co-localization of quantitative trait loci for pod and kernel traits and development of molecular marker for kernel weight on chromosome Arahy05 in peanut (Arachis hypogaea L.)

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