Optimizing plant architecture is essential for improving mechanized harvesting and yield potential in peanut (Arachis hypogaea L.), yet its genetic basis remains unclear. This study aimed to identify stable major-effect QTL associated with main stem length, basal branch length, and the main stem length to basal branch length ratio, and to predict candidate genes using gene expression data and genome sequencing. A previously constructed population of recombinant inbred lines (RIL) derived from a cross between erect-type JH5 and bunch-type KX01-6 was evaluated across three field environments. Statistical analysis identified six QTL with LOD scores ranging from 3.27 to 9.77, explaining 6.14%–24.14% of the phenotypic variation. Among them, qMSL_B09, qBBL_B09, qBBL_B05, and qMBR_B05 were identified in at least two environments. By integrating QTL analysis based on Best Linear Unbiased Prediction (BLUP) values, we narrowed these four stable QTL to two loci, Rpa1 (Regulating plant architecture 1) and Rph1 (Regulating plant height 1) that were delimited to a ~6.840 Mb region (B05: 154.040 Mb to the end) and a ~400 kb physical interval (B09: 158.05–158.45 Mb), respectively. Phenotypic validation using near-isogenic lines (NILs) demonstrated that Rpa1 increased basal branch length by 27.22% and branch angle by 140.08%, while reducing the main stem-to-branch ratio by 22.91%. In contrast, Rph1 decreased main stem length by 42.31% and basal branch length by 46.84%. Map-based cloning of Rph1 identified an 1816-bp deletion in parental line JH5 that influenced the expression of two candidate genes: Ah19g561300 (encoding a bifunctional inhibitor/lipid-transfer protein) and Ah19g561500 (encoding a proteasome subunit). A diagnostic InDel marker to facilitate marker-assisted selection for ideal plant height in breeding programs was developed to track the deletion. Haplotype analysis of 241 accessions confirmed the association of Rph1 with plant architecture, and accessions carrying Haprph1 exhibited significantly higher main stem and basal branch lengths (by ~10%; P < 0.01). These findings provide novel genetic insights and molecular tools for improving plant architecture and enhancing yield potential in peanut.
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High quality is a critical objective in peanut breeding. However, the poor genetic base of cultivated peanuts has significantly limited the breeding efficiency for high-quality peanut. Therefore, unearthing valuable allelic gene resources associated with quality traits would provide basis for expanding genetic diversity of cultivated peanut germplasm resources.
A wild peanut (Arachis villosa), PI 210553, carried diploid A type genome, was used as a donor parent for crossing with cultivated peanuts. Ultra-high oil peanut germplasm with wild ancestry was selected from the progeny, and a recombinant inbred line (RIL) population, derived from this germplasm and the cultivated variety Jihua 5, was used for genetic dissection and QTL mapping of four quality traits across three environments.
Four ultra-high oil accessions of the SW9721 series were selected from the cross population between Yueyou 551 and PI 210553. Notably, SW9721-3 showcased an oil content of 62.50%, exceeding the national high-oil-content peanut standard by 7.5 percent points. Phenotypic analysis of the RIL population revealed that environmental influences caused variations in the mean values of quality traits from 11.02% to 40.80%. Correlation coefficients among these traits varied from 0.23 to 0.97 (P<0.001), with significant associations observed between oil and protein contents, and between oleic and linoleic acid contents. Furthermore, the phenotypic variation of quality traits was found to be between 3.78% and 10.61%, with heritability values above 0.6, absolute values of skewness and kurtosis were less than 1. These phenotypic values were approximately normally distributed, indicating that these traits are quantitatively inherited. In addition, a total of 12 QTLs were identified across the three environments, with LOD scores ranging from 3.26 to 17.82, accounting for 1.97% to 24.56% of the phenotypic variation. Particularly, The QTL locus qPOC_7 was consistently detected in all environments, with LOD scores between 6.01 and 17.82, explaining 4.59% to 24.56% of the phenotypic variation in both protein and oil content. The oil content increase was attributed to the allele from SW9721-3, highlighting the significant breeding value of this QTL. The physical position of flanking molecular markers for qPOC_7 suggested that the corresponding genes are located within a 180 kb interval from 426 363 to 606 659 bp at the end of chromosome 7. Within this candidate region, 22 annotated genes were identified, including two glucose metabolism-related genes, Ah.CKCA5J and Ah.805HV8, which are considered the high-potential candidate genes.
In summary, this study successfully developed an ultra-high oil peanut germplasm, SW9721-3, and identified a major QTL locus, qPOC_7, with significant implications for peanut breeding.
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