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Development and deployment of a high-density linkage map identified quantitative trait loci for plant height in peanut (Arachis hypogaea L.).
Sci Rep. 2016 12 20; 6:39478.SR

Abstract

Plant height is one of the most important architecture traits in crop plants. In peanut, the genetic basis of plant height remains ambiguous. In this context, we genotyped a recombinant inbred line (RIL) population with 140 individuals developed from a cross between two peanut varieties varying in plant height, Zhonghua 10 and ICG 12625. Genotyping data was generated for 1,175 SSR and 42 transposon polymorphic markers and a high-density genetic linkage map was constructed with 1,219 mapped loci covering total map length of 2,038.75 cM i.e., accounted for nearly 80% of the peanut genome. Quantitative trait locus (QTL) analysis using genotyping and phenotyping data for three environments identified 8 negative-effect QTLs and 10 positive-effect QTLs for plant height. Among these QTLs, 8 QTLs had a large contribution to plant height that explained ≥10% phenotypic variation. Two major-effect consensus QTLs namely cqPHA4a and cqPHA4b were identified with stable performance across three environments. Further, the allelic recombination of detected QTLs proved the existence of the phenomenon of transgressive segregation for plant height in the RIL population. Therefore, this study not only successfully reported a high-density genetic linkage map of peanut and identified genomic region controlling plant height but also opens opportunities for further gene discovery and molecular breeding for plant height in peanut.

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Authors+Show Affiliations

Huang L
Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China.
Ren X
Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China.
Wu B
Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China.
Li X
Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China.
Chen W
Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China.
Zhou X
Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China.
Chen Y
Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China.
Pandey MK
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
Jiao Y
Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China.
Luo H
Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China.
Lei Y
Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China.
Varshney RK
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
Liao B
Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China.
Jiang H
Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China.

MeSH

AllelesAnalysis of VarianceArachisChromosome MappingChromosomes, PlantEpistasis, GeneticGenes, PlantGenetic LinkageGenetic MarkersGenotypeMicrosatellite RepeatsModels, StatisticalPhenotypePolymorphism, GeneticQuantitative Trait LociRecombination, Genetic

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

27995991

Citation

Huang, Li, et al. "Development and Deployment of a High-density Linkage Map Identified Quantitative Trait Loci for Plant Height in Peanut (Arachis Hypogaea L.)." Scientific Reports, vol. 6, 2016, p. 39478.
Huang L, Ren X, Wu B, et al. Development and deployment of a high-density linkage map identified quantitative trait loci for plant height in peanut (Arachis hypogaea L.). Sci Rep. 2016;6:39478.
Huang, L., Ren, X., Wu, B., Li, X., Chen, W., Zhou, X., Chen, Y., Pandey, M. K., Jiao, Y., Luo, H., Lei, Y., Varshney, R. K., Liao, B., & Jiang, H. (2016). Development and deployment of a high-density linkage map identified quantitative trait loci for plant height in peanut (Arachis hypogaea L.). Scientific Reports, 6, 39478. https://doi.org/10.1038/srep39478
Huang L, et al. Development and Deployment of a High-density Linkage Map Identified Quantitative Trait Loci for Plant Height in Peanut (Arachis Hypogaea L.). Sci Rep. 2016 12 20;6:39478. PubMed PMID: 27995991.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Development and deployment of a high-density linkage map identified quantitative trait loci for plant height in peanut (Arachis hypogaea L.). AU - Huang,Li, AU - Ren,Xiaoping, AU - Wu,Bei, AU - Li,Xinping, AU - Chen,Weigang, AU - Zhou,Xiaojing, AU - Chen,Yuning, AU - Pandey,Manish K, AU - Jiao,Yongqing, AU - Luo,Huaiyong, AU - Lei,Yong, AU - Varshney,Rajeev K, AU - Liao,Boshou, AU - Jiang,Huifang, Y1 - 2016/12/20/ PY - 2016/06/20/received PY - 2016/11/23/accepted PY - 2016/12/21/entrez PY - 2016/12/21/pubmed PY - 2018/7/14/medline SP - 39478 EP - 39478 JF - Scientific reports JO - Sci Rep VL - 6 N2 - Plant height is one of the most important architecture traits in crop plants. In peanut, the genetic basis of plant height remains ambiguous. In this context, we genotyped a recombinant inbred line (RIL) population with 140 individuals developed from a cross between two peanut varieties varying in plant height, Zhonghua 10 and ICG 12625. Genotyping data was generated for 1,175 SSR and 42 transposon polymorphic markers and a high-density genetic linkage map was constructed with 1,219 mapped loci covering total map length of 2,038.75 cM i.e., accounted for nearly 80% of the peanut genome. Quantitative trait locus (QTL) analysis using genotyping and phenotyping data for three environments identified 8 negative-effect QTLs and 10 positive-effect QTLs for plant height. Among these QTLs, 8 QTLs had a large contribution to plant height that explained ≥10% phenotypic variation. Two major-effect consensus QTLs namely cqPHA4a and cqPHA4b were identified with stable performance across three environments. Further, the allelic recombination of detected QTLs proved the existence of the phenomenon of transgressive segregation for plant height in the RIL population. Therefore, this study not only successfully reported a high-density genetic linkage map of peanut and identified genomic region controlling plant height but also opens opportunities for further gene discovery and molecular breeding for plant height in peanut. SN - 2045-2322 UR - https://www.unboundmedicine.com/medline/citation/27995991/Development_and_deployment_of_a_high_density_linkage_map_identified_quantitative_trait_loci_for_plant_height_in_peanut__Arachis_hypogaea_L___ DB - PRIME DP - Unbound Medicine ER -