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ARS Home » Southeast Area » Tifton, Georgia » Crop Genetics and Breeding Research » Research » Research Project #445194

Research Project: Genomics and Genetic Improvement of Crop Resistance to Multiple Biotic and Abiotic Stresses in Peanut

Location: Crop Genetics and Breeding Research

Project Number: 6048-21000-032-000-D
Project Type: In-House Appropriated

Start Date: Feb 28, 2023
End Date: Feb 27, 2028

Objective 1: Develop advanced peanut parental populations for genomic study, trait discovery, and breeding programs with abiotic and biotic resistance against drought stress, climate change, and diseases such as Tomato spotted wilt virus, early leaf spot, late leaf spot, and root-knot nematode. Objective 2: Integrate molecular markers linked to such traits as TSWV, leaf spots, and root-knot nematode, along with improved drought tolerance, in breeding selection, and pyramid multiple traits for superior peanut germplasm development. Sub-objective 2A: Construct high resolution genetic and trait maps using SNP (single nucleotide polymorphism) markers for fine mapping of QTLs/markers linked to the traits of interest using MAGIC. Sub-objective 2B: Apply molecular markers in breeding and trait stacking/pyramiding to develop superior lines of peanut using a marker assisted recurrent selection (MARS) breeding scheme.

1. Development and maintenance of a large multi-parent advanced generation inter-crosses (MAGIC) peanut population will be used as a new genetic and genomic resource for high-definition trait mapping and breeding selection for high-yielding lines with resistance to biotic and abiotic stresses. Identifying natural allelic variation that underlies quantitative trait variation remains a challenge in genetic studies. Development and phenotypic evaluation of a multi-parental MAGIC mapping population, along with high density genotyping tools and improved bioinformatics for accurate SNP calling will be essential for QTL/marker and trait mapping analyses. 2. Applying the next-generation sequencing technology to develop high-density genetic linkage map for fine-mapping QTLs and identification of underlying gene(s) with SNP markers closely linked to the traits of interest. The resolution of genetic mapping is often insufficient to pinpoint causal genes in bi-parental and smaller-sized populations. The newly developed peanut MAGIC population with eight parental founders will be used to conduct high-resolution mapping of quantitative traits. This MAGIC population comprises 2775 F6 recombinant inbred lines (RILs). A subset of 310 RILs will be randomly selected for replicated field evaluation for diseases and other phenotypic traits, in a randomized complete block (RCB) design with at least three replicates. The phenotypic data will be used for genome mapping of the causal QTLs or genes. The genotyping will be conducted by whole genome re-sequencing, and SNPs and variants will be called using a new sequence analysis pipeline KHUFU. 3. Marker assisted recurrent selection (MARS) is more effective at improving quantitative traits and could accumulate favorable alleles from several genomic regions within a single population. Recurrent selection is defined as re-selection generation after generation, with inter-mating of selected lines, such as recombinant inbred lines (RILs), to produce the population for the next cycle of selection. There are two methods using MAS in breeding selection for breeders. One method is considered in the case of backcross breeding, MAS as a means of reducing linkage drag. The other method is a selection-index method to select, among RILs, those to be crossed to obtain single genotypes containing as many accumulated advantageous alleles as possible using MARS. Recurrent selection is an efficient breeding method for increasing the frequency of superior genes for various economic characters.