Location: Crop Genetics and Breeding ResearchTitle: Recombination bin-map facilitates identification of major QTL on chromosome A01 and potential candidate genes for resistance to Tomato spotted wilt virus in peanut (Arachis hypogaea)
|AGARWAL, GAURAV - University Of Georgia|
|CLEVENGER, JOSH - University Of Georgia|
|KALE, SANDIP - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India|
|WANG, HUI - University Of Georgia|
|PANDEY, MANISH - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India|
|CHOUDHARY, DIVYA - University Of Georgia|
|YUAN, MEI - Shandong Academy Of Agricultural Sciences|
|WANG, XINGJUN - Shandong Academy Of Agricultural Sciences|
|CULBREATH, ALBERT - University Of Georgia|
|Holbrook, Carl - Corley|
|LUI, XIN - Bgi Shenzhen|
|JACKSON, SCOTT - University Of Georgia|
|VARSHNEY, RAJEEV - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India|
Submitted to: Nature Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/17/2019
Publication Date: 12/3/2019
Citation: Agarwal, G., Clevenger, J., Kale, S.M., Wang, H., Pandey, M.K., Choudhary, D., Yuan, M., Wang, X., Culbreath, A.K., Holbrook Jr, C.C., Lui, X., Jackson, S.A., Varshney, R.K., Guo, B. 2019. Recombination bin-map facilitates identification of major QTL on chromosome A01 and potential candidate genes for resistance to Tomato spotted wilt virus in peanut (Arachis hypogaea). Journal of Experimental Botany. 9:18246. https://doi.org/10.1038/s41598-019-54747-1.
Interpretive Summary: Cultivated peanut is an economically important legume crop and serve as a major source of protein and vegetable oil for human nutrition. However, its productivity is severely challenged by foliar diseases such as Tomato spotted wilt virus (TSWV). TSWV has a major impact in southeastern U.S. peanut growing areas including Georgia, Florida and Alabama, resulting in an annual loss of million dollars. In this study, we report the development of the first recombination bin-based genetic map using single nucleotide polymorphism (SNP) markers. Two parental lines were sequenced at greater depth to identify reliable SNPs, and the RILs were sequenced at lower depth. Using this data, the first bin-based genetic linkage map was constructed with 5,816 bins which represented a total of 11,106 SNP markers. Utility of this bin mapping has resulted in identification of major quantitative trait loci (QTL) and candidate genes associated with disease resistance to TSWV, which was all on Chromosome A01. For molecular breeding use, the user-friendly SNP markers associated with the major QTLs were developed that could be used as diagnostic markers in molecular marker-assisted selection (MAS) applications in breeding programs.
Technical Abstract: Peanut (Arachis hypogaea) cultivars released in recent years are crucial to have some levels of resistance to Tomato spotted wilt virus (TSWV), a devastating disease to peanut growers in the Southeastern region of the United States. A recombinant inbred line (RIL) mapping population derived from the cross of SunOleic 97R and NC94022, a high oleic fatty acid runner-type cultivar and a breeding line with the highest level of field resistance to TSWV, respectively, was used in this study to identify the QTLs associated with the resistance. Whole genome re-sequencing was performed on the parents and 140 RILs. A genetic linkage bin-map was constructed, containing 5,816 bins and 20 linkage groups, which represented 11,106 single nucleotide polymorphism (SNP) markers. Using this bin-map, we identified three QTLs associated with resistance to TSWV, which were all on chromosome A01. One QTL with the largest contribution of 36.51% to the phenotypic variation was within physical distance of 89.5 Kb. This genome region harbors a cluster of genes coding for chitinase family protein, strictosidine synthase-like protein, and LRR receptor kinase. SNPs associated with this QTL were used to develop KASP markers, and the validated KASP markers can be deployed in breeding programs. Therefore, this high-density genetic bin-map and QTL linked to resistance to TSWV lay the foundation for possible functional gene mapping, cloning and marker-assisted breeding selection.