Development and evaluation of the utility of GenoBaits Peanut 40K for a peanut MAGIC population

Sun, Ziqi; Zheng, Zheng; Qi, Feiyan; Wang, Juan; Wang, Mengmeng; Zhao, Ruifang; Liu, Hua; Xu, Jing; Qin, Li; Dong, Wenzhao; Huang, Bingyan; Han, Suoyi; Zhang, Xinyou

doi:10.1007/s11032-023-01417-w

Mol Breeding

2023

DOI: 10.1007/s11032-023-01417-w

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Development and evaluation of the utility of GenoBaits Peanut 40K for a peanut MAGIC population

Ziqi Sun,

Zheng Zheng,

Feiyan Qi

et al.

Abstract: Population and genotype data are essential for genetic mapping. The multi-parent advanced generation intercross (MAGIC) population is a permanent mapping population used for precisely mapping quantitative trait loci. Moreover, genotyping-by-target sequencing (GBTS) is a robust high-throughput genotyping technology characterized by its low cost, flexibility, and limited requirements for information management and support. In this study, an 8-way MAGIC population was constructed using eight elite founder lines. … Show more

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2024

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Cited by 4 publications

References 40 publications

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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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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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Development and application of the GenoBaits WheatSNP16K array to accelerate wheat genetic research and breeding

Liu,

Xiang,

Wang

et al. 2024

Plant Communications

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Genome-Wide Association Study Reveals Marker–Trait Associations for Heat-Stress Tolerance in Sweet Corn

Yang,

Guo,

Zhang

et al. 2024

Agronomy

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Sweet corn (Zea mays var. rugosa Bonaf.) is a crop with a high economic benefit in tropical and subtropical regions. Heat tolerance analysis and heat-tolerant gene mining are of great significance for breeding heat-resistant varieties. By combining improved genotyping using targeted sequencing (GBTS) with liquid chip (LC) technology, a high-density marker array containing 40 K multiple single polynucleotide polymorphisms (mSNPs) was used to genotype 376 sweet corn inbred lines and their heat-stress tolerance was evaluated in the spring and summer of 2019. In general, plant height, ear height and the number of lateral branches at the first level of the male flowers were reduced by 24.0%, 36.3%, and 19.8%, respectively. High temperatures in the summer accelerated the growth process of the sweet corn, shortening the days to shedding pollen by an average of 21.6% compared to the spring. A genome-wide association study (GWAS) identified 85 significant SNPs distributed on 10 chromosomes. Phenotypes in the spring and summer were associated with the 21 and 15 loci, respectively, and significant phenotypic differences between the two seasons caused by the temperature change were associated with the 49 SNP loci. The seed setting rate (SSR) was more susceptible to heat stress. An annotation analysis identified six candidate genes, which are either heat shock transcription factors (Hsfs) or heat shock proteins (Hsps) in Arabidopsis and rice (Oryza sativa), and these candidate genes were directly and indirectly involved in the heat-resistant response in the sweet corn. The current findings provide genetic resources for improving the heat-stress tolerance of sweet corn by molecular breeding.

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Development and evaluation of the utility of GenoBaits Peanut 40K for a peanut MAGIC population

Cited by 4 publications

References 40 publications

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.)

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.)

Development and application of the GenoBaits WheatSNP16K array to accelerate wheat genetic research and breeding

Genome-Wide Association Study Reveals Marker–Trait Associations for Heat-Stress Tolerance in Sweet Corn

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