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

Summary Multiparental genetic mapping populations such as nested‐association mapping (NAM) have great potential for investigating quantitative traits and associated genomic regions leading to rapid discovery of candidate genes and markers. To demonstrate the utility and power of this approach, two N...

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Bibliographic Details
Published in:Plant biotechnology journal 2020-06, Vol.18 (6), p.1457-1471
Main Authors: Gangurde, Sunil S., Wang, Hui, Yaduru, Shasidhar, Pandey, Manish K., Fountain, Jake C., Chu, Ye, Isleib, Thomas, Holbrook, C. Corley, Xavier, Alencar, Culbreath, Albert K., Ozias‐Akins, Peggy, Varshney, Rajeev K., Guo, Baozhu
Format: Article
Language:English
Subjects:
Arachis hypogaea
association mapping
candidate genes
Chromosomes
Dissection
Gene mapping
Genes
Genetic control
Genomes
linkage mapping
nested‐association mapping
peanut
Peanuts
pod weight
Population
Population genetics
Populations
Quantitative trait loci
seed weight
Single-nucleotide polymorphism
Weight
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Summary:Summary Multiparental genetic mapping populations such as nested‐association mapping (NAM) have great potential for investigating quantitative traits and associated genomic regions leading to rapid discovery of candidate genes and markers. To demonstrate the utility and power of this approach, two NAM populations, NAM_Tifrunner and NAM_Florida‐07, were used for dissecting genetic control of 100‐pod weight (PW) and 100‐seed weight (SW) in peanut. Two high‐density SNP‐based genetic maps were constructed with 3341 loci and 2668 loci for NAM_Tifrunner and NAM_Florida‐07, respectively. The quantitative trait locus (QTL) analysis identified 12 and 8 major effect QTLs for PW and SW, respectively, in NAM_Tifrunner, and 13 and 11 major effect QTLs for PW and SW, respectively, in NAM_Florida‐07. Most of the QTLs associated with PW and SW were mapped on the chromosomes A05, A06, B05 and B06. A genomewide association study (GWAS) analysis identified 19 and 28 highly significant SNP–trait associations (STAs) in NAM_Tifrunner and 11 and 17 STAs in NAM_Florida‐07 for PW and SW, respectively. These significant STAs were co‐localized, suggesting that PW and SW are co‐regulated by several candidate genes identified on chromosomes A05, A06, B05, and B06. This study demonstrates the utility of NAM population for genetic dissection of complex traits and performing high‐resolution trait mapping in peanut.
ISSN:1467-7644
1467-7652
DOI:10.1111/pbi.13311