Dataset Information

Construction of High-Density Genetic Map and Mapping Quantitative Trait Loci for Growth Habit-Related Traits of Peanut (Arachis hypogaea L.).

ABSTRACT: Plant growth habit is an important and complex agronomic trait and is associated with yield, disease resistance, and mechanized harvesting in peanuts. There are at least two distinct growth habits (erect and prostrate) and several intermediate forms existing in the peanut germplasm. A recombinant inbred line population containing 188 individuals was developed from a cross of "Jihua 5" and "M130" for genetically dissecting the architecture of the growth habit. A new high-density genetic linkage map was constructed by using specific locus amplified fragment sequencing technology. The map contains 2,808 single-nucleotide polymorphism markers distributed on 20 linkage groups with a total length of 1,308.20 cM and an average inter-marker distance of 0.47 cM. The quantitative trait locus (QTL) analysis of the growth habit-related traits was conducted based on phenotyping data from seven environments. A total of 39 QTLs for growth habit-related traits was detected on 10 chromosomes explaining 4.55-27.74% of the phenotypic variance, in which 6 QTLs were for lateral branch angle, 8 QTLs were for extent radius, 7 QTLs were for the index of plant type, 11 QTLs were for main stem height, and 7 QTLs were for lateral branch length. Among these QTLs, 12 were co-localized on chromosome B05 spanning an approximately 0.17 Mb physical interval in comparison with the allotetraploid reference genome of "Tifrunner." Analysis of the co-localized genome region has shown that the putative genes are involved in light and hormones and will facilitate peanut growth habit molecular breeding and study of peanut domestication.

SUBMITTER: Li L

PROVIDER: S-EPMC6584813 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Publications

Construction of High-Density Genetic Map and Mapping Quantitative Trait Loci for Growth Habit-Related Traits of Peanut (<i>Arachis hypogaea</i> L.).

Li Li L Yang Xinlei X Cui Shunli S Meng Xinhao X Mu Guojun G Hou Mingyu M He Meijing M Zhang Hui H Liu Lifeng L Chen Charles Y CY

Frontiers in plant science 20190612

Plant growth habit is an important and complex agronomic trait and is associated with yield, disease resistance, and mechanized harvesting in peanuts. There are at least two distinct growth habits (erect and prostrate) and several intermediate forms existing in the peanut germplasm. A recombinant inbred line population containing 188 individuals was developed from a cross of "Jihua 5" and "M130" for genetically dissecting the architecture of the growth habit. A new high-density genetic linkage m ...[more]

PMID: 31263472

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Project description:BackgroundThe cultivated peanut is an important oil and cash crop grown worldwide. To meet the growing demand for peanut production each year, genetic studies and enhanced selection efficiency are essential, including linkage mapping, genome-wide association study, bulked-segregant analysis and marker-assisted selection. Specific locus amplified fragment sequencing (SLAF-seq) is a powerful tool for high density genetic map (HDGM) construction and quantitative trait loci (QTLs) mapping. In this study, a HDGM was constructed using SLAF-seq leading to identification of QTL for seed weight and size in peanut.ResultsA recombinant inbred line (RIL) population was advanced from a cross between a cultivar 'Huayu36' and a germplasm line '6-13' with contrasting seed weight, size and shape. Based on the cultivated peanut genome, a HDGM was constructed with 3866 loci consisting of SLAF-seq and simple sequence repeat (SSR) markers distributed on 20 linkage groups (LGs) covering a total map distance of 1266.87 cM. Phenotypic data of four seed related traits were obtained in four environments, which mostly displayed normal distribution with varied levels of correlation. A total of 27 QTLs for 100 seed weight (100SW), seed length (SL), seed width (SW) and length to width ratio (L/W) were identified on 8 chromosomes, with LOD values of 3.16-31.55 and explaining phenotypic variance (PVE) from 0.74 to 83.23%. Two stable QTL regions were identified on chromosomes 2 and 16, and gene content within these regions provided valuable information for further functional analysis of yield component traits.ConclusionsThis study represents a new HDGM based on the cultivated peanut genome using SLAF-seq and SSRs. QTL mapping of four seed related traits revealed two stable QTL regions on chromosomes 2 and 16, which not only facilitate fine mapping and cloning these genes, but also provide opportunity for molecular breeding of new peanut cultivars with improved seed weight and size.

Project description:BackgroundAllergic reactions to peanuts (Arachis hypogaea L.) can cause severe symptoms and in some cases can be fatal, but avoidance is difficult due to the prevalence of peanut-derived products in processed foods. One strategy of reducing the allergenicity of peanuts is to alter or eliminate the allergenic proteins through mutagenesis. Other seed quality traits could be improved by altering biosynthetic enzyme activities. Targeting Induced Local Lesions in Genomes (TILLING), a reverse-genetics approach, was used to identify mutations affecting seed traits in peanut.ResultsTwo similar copies of a major allergen gene, Ara h 1, have been identified in tetraploid peanut, one in each subgenome. The same situation has been shown for major allergen Ara h 2. Due to the challenge of discriminating between homeologous genes in allotetraploid peanut, nested PCR was employed, in which both gene copies were amplified using unlabeled primers. This was followed by a second PCR using gene-specific labeled primers, heteroduplex formation, CEL1 nuclease digestion, and electrophoretic detection of labeled fragments. Using ethyl methanesulfonate (EMS) as a mutagen, a mutation frequency of 1 SNP/967 kb (3,420 M2 individuals screened) was observed. The most significant mutations identified were a disrupted start codon in Ara h 2.02 and a premature stop codon in Ara h 1.02. Homozygous individuals were recovered in succeeding generations for each of these mutations, and elimination of Ara h 2.02 protein was confirmed. Several Ara h 1 protein isoforms were eliminated or reduced according to 2D gel analyses. TILLING also was used to identify mutations in fatty acid desaturase AhFAD2 (also present in two copies), a gene which controls the ratio of oleic to linoleic acid in the seed. A frameshift mutation was identified, resulting in truncation and inactivation of AhFAD2B protein. A mutation in AhFAD2A was predicted to restore function to the normally inactive enzyme.ConclusionsThis work represents the first steps toward the goal of creating a peanut cultivar with reduced allergenicity. TILLING in peanut can be extended to virtually any gene, and could be used to modify other traits such as nutritional properties of the seed, as shown in this study.

Dataset Information

Construction of High-Density Genetic Map and Mapping Quantitative Trait Loci for Growth Habit-Related Traits of Peanut (Arachis hypogaea L.).

Publications

Construction of High-Density Genetic Map and Mapping Quantitative Trait Loci for Growth Habit-Related Traits of Peanut (<i>Arachis hypogaea</i> L.).

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