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

Sunil S Gangurde,Peggy Ozias‐Akins,Hui Wang,Jake C Fountain,C Corley Holbrook,Ye Chu,Baozhu Guo,Shasidhar Yaduru,Albert K Culbreath,Manish K Pandey,Rajeev K Varshney,Thomas Isleib,Alencar Xavier

doi:10.1111/pbi.13311

Abstract

SummaryMultiparental 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.

Highlights

Peanut (Arachis hypogaea L.) is a cash crop with high market and nutritional values
Phenotypic variation for pod weight and seed weight in nested-association mapping (NAM) populations Significant variation was recorded for 100 pod weight (PW) and 100 seed weight (SW), and the mid-parental values for PW and SW were close to the population mean
Transgressive segregants were observed for PW and SW among the recombinant inbred line (RIL), indicating multigenic inheritance of the traits

Summary

Introduction

Peanut (Arachis hypogaea L.) is a cash crop with high market and nutritional values. The major focus of breeding is to increase the yield, which is directly proportional to the number of pods per plant, pod weight and seed weight (Gomes and Lopez, 2005). Preferences related to traits such as oil contents, oleic acid contents, relatively large seed size and testa colour drive demand from industries and consumers ensuring higher prices in national and international markets (Gangurde et al, 2019; Venuprasad et al, 2011). Earlier reports on correlation between seed mass, oil and protein contents showed linear increases in oil and protein contents with increased seed mass (Dwivedi et al, 1990). Significant variation is available in the cultivated gene pool for seed weight, and several conventional breeding programs are targeting for large-seeded peanut (Venuprasad et al, 2011). Others suggested quantitative inheritance of seed weight with additive gene action (Garet, 1976), epistatic effects (Upadhyaya et al, 1992) or maternal inheritance (Hariprasanna et al, 2008)

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