Genome-wide landscapes of genes and repeatome reveal the genomic differences between the two subspecies of peanut (Arachis hypogaea)

Bhat, Ramesh; Shirasawa, Kenta; Gangurde, Sunil S.; Rashmi, Mayank; Sahana, K. P.; Pandey, Manish K.

doi:10.1016/j.cropd.2023.100029

Cited by 1 publication

(1 citation statement)

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“…By selecting polymorphic markers between RIL parents in our resequencing data and predicting their impact on gene functions, an INDEL in the coding sequence of Arahy.JX1V6X and a SNP in the coding sequence of Arahy.P2ZS9F were both polymorphic between the RIL parents and predicted to have moderate or high impact on functions of these genes (Table 2 ). Meanwhile, the INDEL and SNP variants closely linked with kernel traits were not likely due to genetic structure from two subspecies of cultivated peanut as indicated by a recent study [ 33 ]. The INDEL marker was validated by PCR in 31 RILs and was closely linked with HKW (Table 3 ).…”

Section: Discussionmentioning

confidence: 99%

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

Fang,

Liu,

Qin

et al. 2023

BMC Genomics

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Peanut (Arachis hypogaea L.) is an important oilseed crop worldwide. Improving its yield is crucial for sustainable peanut production to meet increasing food and industrial requirements. Deciphering the genetic control underlying peanut kernel weight and size, which are essential components of peanut yield, would facilitate high-yield breeding. A high-density single nucleotide polymorphism (SNP)-based linkage map was constructed using a recombinant inbred lines (RIL) population derived from a cross between the variety Yuanza9102 and a germplasm accession wt09-0023. Kernel weight and size quantitative trait loci (QTLs) were co-localized to a 0.16 Mb interval on Arahy07 using inclusive composite interval mapping (ICIM). Analysis of SNP, and Insertion or Deletion (INDEL) markers in the QTL interval revealed a gene encoding a pentatricopeptide repeat (PPR) superfamily protein as a candidate closely linked with kernel weight and size in cultivated peanut. Examination of the PPR gene family indicated a high degree of collinearity of PPR genes between A. hypogaea and its diploid progenitors, Arachis duranensis and Arachis ipaensis. The candidate PPR gene, Arahy.JX1V6X, displayed a constitutive expression pattern in developing seeds. These findings lay a foundation for further fine mapping of QTLs related to kernel weight and size, as well as validation of candidate genes in cultivated peanut.

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Section: Discussionmentioning

confidence: 99%