Location: Crop Genetics and Breeding Research
Project Number: 6048-21000-028-000-D
Project Type: In-House Appropriated
Start Date: Feb 28, 2018
End Date: Feb 27, 2023
Objective:
1. Elucidate the interactions of responses in peanut to multiple biotic and abiotic stress factors, such as drought, tomato spotted wilt virus, leaf spots, white mold, and root-knot nematode; determine overlapping response pathways; discover selection targets (genes or networks); and work with breeders to use the information in developing peanut varieties with broad spectrum stress resistance/tolerance.
1A. Develop next-generation fine-mapping population segregating multiple traits of interest, such as Multi-parent Advanced Generation Inter-Cross (MAGIC), and conduct phenotypes in the field.
1B. Construct high resolution genetic and trait maps using single nucleotide polymorphism (SNP) markers for fine-mapping of QTLs/markers linked to the traits of interest.
1C. Apply molecular markers in breeding and trait stacking/pyramiding to develop superior lines of peanut using Marker Assisted Recurrent Selection (MARS) breeding scheme.
Approach:
1. 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 available, such as newly developed peanut 58K SNP array and/or whole genome re-sequencing (WGRS), will be essential for quantitative trait loci/marker and trait mapping analyses. The primary aim of this objective is to develop the first next-generation fine-mapping population of peanut that can be used by the peanut research community, and to conduct high-resolution phenotyping of this population. Because of the size of the population, as large as 2,000 to 3,000, the entire population will be genotyped. A core subset (or different core subsets) of the entire population will be developed (divided) based on the genetic similarity or based on unique marker scores for different trait (disease resistance). Therefore, the subset of individuals could be manageable in a replicated test in the field or greenhouse for testing a specific trait of disease resistance such as nematode resistance. Drought stress study will include irrigation and non-irrigation.
2. We will use the WGRS approach for the parental lines “SunOleic 97R and NC94022”, “Tifrunner and GT-C20”, and the derived RILs (referred to as the “S” and the “T” populations) to identify the SNPs and genotype the populations. In order to improve the map density and fine-map the QTLs for MAS, we plan to use WGRS approach to genotype this population to improve the genetic map density and to identify genomic regions/candidate genes controlling the resistant traits. SNP marker validation will be conducted through KASP assay. The KASP genotyping assay is a fluorescence based assay for identification of biallelic SNPs. KASP marker data will be analyzed using SNPviewer software (LGC Genomics) (http://www.lgcgroup.com) to generate genotype calls for each RIL and parental line, and were correlated with observed disease ratings (phenotypes) in the field for selection.
3. Recurrent selection is defined as re-selection generation after generation, with inter-mating of selected lines, such as RILs, to produce the population for the next cycle of selection. There are two methods using MAS in breeding selection for breeders. Recurrent selection is an efficient breeding method for increasing the frequency of superior genes for various economic characters. One RIL population described in Sub-objective 1B is the “S” population, and QTL mapping has been completed for targeted traits: total oil content, oil quality, disease resistance to early leaf spot (ELS), late leaf spot (LLS), and TSWV. Therefore, we propose to select eight RIL lines (founders) with known markers/QTL associated with specific traits for inter-crossing in order to stack/pyramid all favorable alleles in peanut breeding for superior cultivars with multiple traits. All traits of interest will be considered concurrently. The goal is to develop superior peanut lines, which have either high oil content (50% or above) or low oil content (40% or less) with high oleic acid and resistance to ELS, LLS, and TSWV.
