Location: Crop Genetics and Breeding Research
2024 Annual Report
Objectives
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.
Approach
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.
Progress Report
The primary focus of this project 6048-21000-032-00D, “Genomics and Genetic Improvement of Crop Resistance to Multiple Biotic and Abiotic Stresses in Peanut,” is to develop next-generation multiparent mapping population as genetic and genomic resources for breeding superior peanut cultivars and for trait fine-mapping and genome studies. [301, 1A, 1B, 2A, 2B, 3A].
Objective 1: Research continued the advancement and seed increase of peanut multiple-parent intercrossed population. The total population is 2775 lines. Two experiments were planted: (1) 1/3 of the total population was planted without replication for seed increase and for initial phenotyping including agronomic performance and reaction to various biotic and abiotic stresses; (2) a subset of 310 lines was randomly selected from the whole population and planted with three replicates along with the eight parent lines and the data collected including disease rating for tomato spotted wilt virus (TSWV), leaf spots, and lesion nematode for further data analysis. All the plots were harvested, and seeds have been inventoried.
Sub-objective 2A, the leaf tissues were collected from the subset lines of 310 and the parents. DNA was extracted for whole genome sequencing with low coverage and the parent DNA was extracted for long-read sequencing. The sequenced genomes have been assembled for further analysis.
Sub-objective 2B: the lines with multiple disease resistance such as leaf spots and TSWV were planted for further evaluation and seed increase. Data of various agronomic traits were collected. The seeds have been harvested and inventoried.
ARS researchers in Tifton, Georgia, in collaboration with scientists in the University of Georgia and Louisiana State University conducted research attempting to employ novel double stranded RNA based gene silencing technology to mitigating Aspergillus flavus fungal infection and subsequent aflatoxin contamination. Progresses made were in selecting targeted genes, designed the constructs, and synthesized 8 sets of primers for amplification. The products were verified and produced for initial testing in the laboratory. Use of these constructs in culture experiments has demonstrated significant reductions in aflatoxin production. The dsRNA production procedures were improved to consistently obtain high quality dsRNAs from bacterial cultures. This subordinate project relates to Objective 1, climate-change exacerbated drought stress and prevention in aflatoxin contamination.
Accomplishments
1. Genetic and genomic characterization of a multiparent advanced generation inter-cross (MAGIC) population. ARS researchers in Tifton, Georgia, developed a multiple parent population called PeanutMAGIC and characterized a subset of 310 lines randomly selected from the whole population using 2-years’ phenotypes of various peanut pod and seed traits and genotypes with whole genome sequencing. The genetic and genomic data suggest that this population has broadened the genetic diversit, produced new recombinants with novel characters, and increased “fine” recombination for potential fine mapping of the resistance genes such as to root-knot nematode and tomato spotted wilt virus (TSWV). This should lead to the development of genetic markers which will enable breeders to develop superior peanut cultivars more effectively.
Review Publications
Knoll, J.E., Perla, T.J., Krakowsky, M.D., Guo, B. 2023. Combining ability of experimental maize lines for yield and aflatoxin in the southeastern United States. Crop Science. 63:2793-2806. https://doi.org/10.1002/csc2.21050.
Ni, X., Huffaker, A., Schmelz, E.A., Xu, W., Williams, W.P., Guo, B., Li, X., Huang, F. 2024. Field evaluation of experimental maize hybrids for resistance to the fall armyworm (Lepidoptera: Noctuidae) in a warm temperate climate. Insects. 15(4):289. https://doi.org/10.3390/insects15040289.
Garg, V., Dudchenko, O., Wang, J., Khan, A.W., Gupta, S., Kaur, P., Han, K., Saxena, R.K., Kale, S.M., Pham, M., Yu, J., Chitikineni, A., Zhang, Z., Fan, G., Lui, C., Valluri, V., Meng, F., Bhandari, A., Liu, X., Yang, T., Chen, H., Valliyodan, B., Roorkiwal, M., Shi, C., Yang, H., Durand, N.C., Pandey, M.K., Li, G., Barmukh, R., Wang, X., Chen, X., Lam, H., Jiang, H., Zong, X., Liang, X., Liu, X., Liao, B., Guo, B., Jackson, S., Nguyen, H.T., Zhuang, W., Wan, S., Wang, X., Aiden, E.L., Bennetzen, J.L., Varshney, R.K. 2021. Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement. Journal of Advanced Research. 42:315-329. https://doi.org/10.1016/j.jare.2021.10.009.
Gangurde, S., Korani, W., Bajaj, P., Wang, H., Fountain, J.C., Agarwal, G., Pandey, M.K., Abbas, H.K., Chang, P., Holbrook Jr, C.C., Kemerait, R.C., Varshney, R.K., Dutta, B., Clevenger, J.P., Guo, B. 2024. Aspergillus flavus pangenome (AflaPan) uncovers novel aflatoxin and secondary metabolite associated gene clusters. BMC Plant Biology. 24:354. https://doi.org/10.1186/s12870-024-04950-8.
Gangurde, S.S., Thompson, E., Yaduru, S., Wang, H., Fountain, J., Chu, Y., Ozias-Akins, P., Isleib, T.G., Holbrook Jr, C.C., Dutta, B., Culbreath, A.K., Pandey, M.K., Guo, B. 2024. Linkage mapping and genome-wide association study identified two peanut late leaf spot resistance loci, PLLSR-1 and PLLSR-2, using nested association mapping. Phytopathology. 114:1346-1355. https://doi.org/10.1094/PHYTO-04-23-0143-R.