Nested-association mapping (NAM)-based genetic dissection uncovers candidate genes for seed and pod weights in peanut (Arachis hypogaea)

Authors: GANGURDE, SUNIL - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; WANG, HUI - University Of Georgia; YADURU, SHASIDHAR - University Of Georgia; PANDEY, MANISH - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; FOUNTAIN, JAKE - University Of Georgia; CHU, YE - University Of Georgia; ISLEIB, THOMAS - North Carolina State University; Holbrook, Carl - Corley; XAVIER, ALENCAR - Corteva Agriscience; CULBREATH, ALBERT - University Of Georgia; OZIAS-AKINS, PEGGY - University Of Georgia; VARSHNEY, RAJEEV - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; Guo, Baozhu

Submitted to: Plant Biotechnology Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/15/2019
Publication Date: 12/5/2019
Citation: Gangurde, S.S., Wang, H., Yaduru, S., Pandey, M.K., Fountain, J.C., Chu, Y., Isleib, T.G., Holbrook Jr, C.C., Xavier, A., Culbreath, A., Ozias-Akins, P., Varshney, R.K., Guo, B. 2019. Nested-association mapping (NAM)-based genetic dissection uncovers candidate genes for seed and pod weights in peanut (Arachis hypogaea). Plant Biotechnology Journal. https://doi.org/10.1111/pbi.13311.
DOI: https://doi.org/10.1111/pbi.13311

Interpretive Summary: Multi-parental genetic population such as nested-association mapping (NAM) population has great potential for investigating quantitative traits and finding their genomic control, leading to faster discovery of candidate genes and markers. UpToDate, only bi-parental and natural populations were used in peanut for conducting trait mapping studies. U.S. peanut research community has developed structured recombinant inbred line (RIL) populations with two runner cultivars (Tifrunner and Florida-07) as common parents. Our objectives were to demonstrate the utility and power of the NAM populations, NAM_Tifrunner and NAM_Florida, by using a subset of the available individual RIL populations developed in peanut community for mapping peanut seed weight (SW) and pod weight (PW). We applied the high-density SNP genotyping assay using 58K peanut SNPs, which further improved the resolution of trait mapping. We carried out the genetic and genome-wide association studies (GWAS) analyses and identified potential genomic regions and candidate genes over eight chromosomes (A05, A06, A08, A09, B05, B06, B08 and B09) for seed weight and pod weight. Identified candidate genes such as spermidine synthase (spds) need to be further investigated to measure accurate impact on these traits in addition to developing markers for assistance in breeding selection for new cultivars with desired seed and pod weight resulting in improved yield.

Technical Abstract: Multi-parental genetic population such as nested-association mapping (NAM) population has great potential for investigating quantitative traits and finding their genomic control leading to faster discovery of candidate genes and markers. Our objectives were to demonstrate the utility and power of the NAM populations, NAM_Tifrunner (581 RILs) and NAM_Florida (496 RILs), by using a subset of the available individual RIL populations developed in peanut community for mapping peanut seed weight (SW) and pod weight (PW). Genetic mapping identified 8 and 12 major effect QTLs for SW and PW, respectively, in NAM_Tifrunner. Similarly, there were 11 and 13 major effect QTLs for SW and PW, respectively, in NAM_Florida. Majority of the QTLs linked to SW and PW were identified on chromosome A05, A06, B05, and B06. Simultaneously, GWAS (genome-wide association mapping study) identified highly significant SNP-trait associations (STAs) for SW and PW. There were 17 and 11 STAs identified for SW and PW, respectively, in NAM_Florida, whereas 28 and 19 STAs were identified for SW and PW in NAM_Tifrunner. These results reported that the quantitative traits of SW and PW in peanut are regulated by genes located on chromosomes A05, A06, B05, and B06, and also facilitated discovery of potential candidate genes such as spermidine synthase (spds), nodulins, E2F transcription factors, STERILE APPETELLA proteins, protein kinases, acyl co-A synthatases, MYB transcription factors, and pentatricopeptide repeat (PPR). This study also demonstrates the utility of NAM for genetic dissection of complex traits and supports the power of the NAM population for high resolution trait mapping in peanut.