Scientia Agricultura Sinica ›› 2017, Vol. 50 ›› Issue (2): 228-239.doi: 10.3864/j.issn.0578-1752.2017.02.003

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Genome Wide Association Analysis of Silique Length in Brassica napus L.

ZHOU QingHong1, ZHOU Can1, ZHENG Wei2, FU DongHui1   

  1. 1 College of Agronomy, Jiangxi Agricultural University/The Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Nanchang 330045; 2Jiangxi Institute of Red Soil, Jinxian 331717, Jiangxi
  • Received:2016-07-19 Online:2017-01-16 Published:2017-01-16

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Abstract: 【Objective】The objective of this study is to detect the SNP loci and determine related candidate genes affecting the silique length of B. napus significantly to reveal its genetic basis and molecular mechanism, and lay a foundation for the marker assisted selection in high yield breeding of B. napus. 【Method】In this study, the phenotype of silique length was investigated at two environments (JXAU of Nanchang and JXIRS of Jinxian) with 300 accessions of B. napus, combining with the 201,817 SNPs developed from specific locus amplified fragment sequencing (SLAF-seq) technology, the genome-wide association analysis was proceeded to detect the SNP loci affecting the silique length significantly, and the regions were scanned with 100 kb apart from the loci of SNP associated dramatically with silique length based on linkage disequilibrium analysis, and finally the candidate genes were predicted with relation to silique length by BLAST analysis.【Result】The variation ranges of silique length in the two places were 46.35-107.07 mm and 39.41-101.35 mm, respectively, which both showed extensive phenotypic variation in two environments. In addition, a total of 121 SNP loci in JXAU correlatively with silique length were excavated by general linear model (GLM), which distributed on A04, A06, A08, A09, C02, C03, C06 and C09 chromosomes, and the largest number of SNPs (83) was on A09 chromosome. Otherwise, 22 SNPs in JXIRS with 1 on C09 and 21 on A09 were detected, and there were 20 consensus SNPs under two environments. Besides, 5 SNPs in JXAU and 3 SNPs (P＜4.96E-07) in JXIRS all distributed on A09 chromosome were detected respectively using the mixed linear model (MLM), three of which were consistent in two environments. There were 40 candidate genes screened in the candidate regions with 100 kb apart from the positions of SNPs associated significantly with silique length, functional analyses showed that these genes involved in regulation of carbohydrate transportation and synthesis, flower and seed development, signal transduction and etc., which might result in the variation of silique length through affecting the growth and development of silique in B. napus. 【Conclusion】The SNP loci and candidate genes related closely with silique length of B. napus were detected in this study, thus providing a theoretical basis for the seed yield regulatory network of B. napus and molecular assisted selection of high-yield breeding of rapeseed.

Key words: Brassica napus, Genome-wide association study, silique length, SNP locus, candidate gene

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