Dissection of the genetic basis of oil content in Chinese peanut cultivars through association mapping

Abstract

Background: Peanut is one of the primary sources for vegetable oil worldwide, and enhancing oil content is the main objective in several peanut breeding programs of the world. Tightly linked markers are required for faster development of high oil content peanut varieties through genomics-assisted breeding (GAB), and association mapping is one of the promising approaches for discovery of such associated markers. Results: An association mapping panel consisting of 292 peanut varieties extensively distributed in China was phenotyped for oil content and genotyped with 583 polymorphic SSR markers. These markers amplified 3663 alleles with an average of 6.28 alleles per locus. The structure, phylogenetic relationship, and principal component analysis (PCA) indicated two subgroups majorly differentiating based on geographic regions. Genome-wide association analysis identified 12 associated markers including one (AGGS1014_2) highly stable association controlling up to 9.94% phenotypic variance explained (PVE) across multiple environments. Interestingly, the frequency of the favorable alleles for 12 associated markers showed a geographic difference. Two associated markers (AGGS1014_2 and AHGS0798) with 6.90-9.94% PVE were verified to enhance oil content in an independent RIL population and also indicated selection during the breeding program. Conclusion: This study provided insights into the genetic basis of oil content in peanut and verified highly associated two SSR markers to facilitate marker-assisted selection for developing high-oil content breeding peanut varieties.

Genome-Wide Association Studies Revealed the Genetic Loci and Candidate Genes of Pod-Related Traits in Peanut (Arachis hypogaea L.)

“…The candidate interval was determined by the LD decay distance, which is related to species reproduction mode, population size, artificial selection and other factors [52]. The average LD decay distance of the population used in this study was 160.3 kb, which was lower than the LD decay distance of the reported peanut populations, and the positioning accuracy was good [6,17,53]. The 136 peanut accessions were geographically widely sourced, which may be the reason for the relatively low LD in this study.…”

An Overview of Mapping Quantitative Trait Loci in Peanut (Arachis hypogaea L.)

“…Three MAGIC populations also were developed by crossing eight parental genotypes targeting multiple traits, including fresh seed dormancy, oil content, aflatoxin, and drought resistance [ 69 ]. Despite the discovery of QTL mainly using linkage analysis, natural population-based mapping has also been used in a couple of studies [ 74 , 75 , 76 , 77 , 78 , 79 , 80 ]. It is discussed in the next section.…”

“… Derivation of biparental and other populations used for peanut. F2 [ 29 , 36 , 43 , 55 , 58 ], BC2F2 [ 15 ], BC1F1 [ 59 ], BC2F4 [ 60 , 61 , 62 ], BC2RIL [ 18 ], BC2F1 [ 63 ], RIL [ 44 , 45 , 46 , 47 , 48 ], CSSL [ 64 , 65 , 66 ], NIL [ 67 ] MAGIC [ 69 , 71 ], NAM [ 69 , 70 , 73 ], Natural population [ 74 , 75 , 76 , 77 , 78 ]. …”

“…The other 107 significant SNP markers underlying pod weight, pod length, pod width, seed length, seed width, and 100-pod weight and 100-seed weight [ 76 , 79 ] were discovered using 158 and 250 genotypes, respectively. Similarly, 12 QTL associated with oil content were identified using 292 accession numbers [ 78 ], and 253 loci controlling oil content, protein content, oleic to linoleic acid ratio, and fatty acid composition were identified [ 77 , 80 ] using 120 and 250 genotypes, respectively. Among all the genotypes that have been used as a mapping population, more than 50% are from core collections.…”

“…It is discussed in the next section. linkage analysis, natural population-based mapping has also been used in a couple of studies [74][75][76][77][78][79][80]. It is discussed in the next section.…”