Development of SSR markers and identification of major quantitative trait loci controlling shelling percentage in cultivated peanut (Arachis hypogaea L.)

• Published in: Theoretical and applied genetics Vol. 130; no. 8; pp. 1635 - 1648
• Main Authors: Luo, Huaiyong, Xu, Zhijun, Li, Zhendong, Li, Xinping, Lv, Jianwei, Ren, Xiaoping, Huang, Li, Zhou, Xiaojing, Chen, Yuning, Yu, Jingyin, Chen, Weigang, Lei, Yong, Liao, Boshou, Jiang, Huifang
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01-08-2017; Springer; Springer Nature B.V
• Subjects: Agriculture; Arachis - genetics; Arachis duranensis; Arachis hypogaea; Arachis ipaensis; Biochemistry; Biological markers; Biomedical and Life Sciences; Biotechnology; Breeding; Chromosome Mapping; Gene loci; Gene mapping; Genetic aspects; Genetic Markers; Genome, Plant; Genomes; Genotype; Genotype & phenotype; Genotyping; Grain; Inbreeding; Life Sciences; Microsatellite Repeats; Observations; Original; Original Article; Peanuts; Phenotype; Phenotyping; Physiological aspects; Plant Biochemistry; Plant Breeding; Plant Breeding/Biotechnology; Plant Genetics and Genomics; Quantitative Trait Loci; Variance; Major Quantitative Trait Locus; Minor QTLs; Phenotypic Variation Explain; Quantitative Trait Locus; Quantitative Trait Locus Analysis
• ISSN: 0040-5752; 1432-2242
• DOI: 10.1007/s00122-017-2915-3

Key message
A total of 204,439 SSR markers were developed in diploid genomes, and 25 QTLs for shelling percentage were identified in a RIL population across 4 years including five consistent QTLs.
Cultivated peanut (
Arachis hypogaea
L.) is an important grain legume providing edible oil and protein for human nutrition. Genome sequences of its diploid ancestors,
Arachis duranensis
and
A. ipaensis
, were reported, but their SSRs have not been well exploited and utilized hitherto. Shelling percentage is an important economic trait and its improvement has been one of the major objectives in peanut breeding programs. In this study, the genome sequences of
A. duranensis
and
A. ipaensis
were used to develop SSR markers, and a mapping population (Yuanza 9102 × Xuzhou 68-4) with 195 recombinant inbred lines was used to map QTLs controlling shelling percentage. The numbers of newly developed SSR markers were 84,383 and 120,056 in the
A. duranensis
and
A. ipaensis
genomes, respectively. Genotyping of the mapping population was conducted with both newly developed and previously reported markers. QTL analysis using the phenotyping data generated in Wuhan across four consecutive years and genotyping data of 830 mapped loci identified 25 QTLs with 4.46–17.01% of phenotypic variance explained in the four environments. Meta-analysis revealed five consistent QTLs that could be detected in at least two environments. Notably, the consistent QTL
cqSPA09
was detected in all four environments and explained 10.47–17.01% of the phenotypic variance. The segregation in the progeny of a residual heterozygous line confirmed that the
cpSPA09
locus had additive effect in increasing shelling percentage. These consistent and major QTL regions provide opportunity not only for further gene discovery, but also for the development of functional markers for breeding.