ACTA AGRICULTURAE BOREALI-SINICA ›› 2019, Vol. 34 ›› Issue (6): 47-53. doi: 10.7668/hbnxb.20191003

• Crop Genetics·Germplasm Resources·Biotechnology • Previous Articles     Next Articles

Rapid Mining Genetic Locus for Controlling Target Traits Using Next-generation Sequencing (NGS)

LIN Jing1,2, ZHAO Qingsong1, ZHANG Mengchen1, YANG Chunyan1, ZHAO Tuanjie2   

  1. 1. Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, National Center for Soybean Improvement, Shijiazhuang Sub-Center, Huang-huai-hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, The Key Laboratory of Crop Genetics and Breeding of Hebei, Shijiazhuang 050035, China;
    2. National Center for Soybean Improvement, Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture, National Key Laboratory for Crop Genetics and Germplasm, Nanjing Agricultural University, Nanjing 210095, China
  • Received:2019-10-15 Published:2019-12-28

Abstract: To rapidly determine the genetic loci for target traits and develop molecular markers linked to traits which could remove plants with disadvantage traits in high generation breeding line and accelerate the breeding process. In this study, a row of F6 generation plants performing flower color segregation were selected from soybean MS recurrent population and individually harvested to form F6:7 population. Among the F6:7 population, 20 and 17 homozygous family lines with purple and white flower color, respectively, were selected to construct two DNA pools. Following, genetic variation were derived from next-generation sequencing and SNP enriched region were determined, furthermore, molecular markers were also developed to confirm the linkage between markers and target traits. High throughput sequencing analysis showed a total of 329 992 SNP variations were identified between the DNA pools of purple and white color, indicating that the genetic background between the DNA pools have a high degree of similarity. However, no significant SNP rich region was found possible due to there exist lots of false positive SNP. After screening SNP variations with high standard (Quality>100) and removing heterozygous SNP variations, a total of 3 371 confidence SNP variation were obtained. Among them, 700 (20.77%) distribute on chromosome 13, and most were clustered in the physical interval of 20 to 30 Mb, strongly indicating that W1 was localized in this region. Two new markers, dCAPS-1, dCAPS-2 in the region were developed and they were linked to W1 closely (W1 -(0.4 cM)-dCAPS-1-(2.3 cM)-dCAPS-2). In conclusion, the locus underlying the target traits could be rapidly determined through constructing two segregation pools from high generation line and genotyping by next-generation sequencing. Moreover, the disadvantage traits could be effective removed by the linked dCAPS markers which will accelerate breeding process.

Key words: Mixture pools of advance line, High-throughput sequencing, SNP variations, Genetic mapping, Molecular marker development

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Cite this article

LIN Jing, ZHAO Qingsong, ZHANG Mengchen, YANG Chunyan, ZHAO Tuanjie. Rapid Mining Genetic Locus for Controlling Target Traits Using Next-generation Sequencing (NGS)[J]. ACTA AGRICULTURAE BOREALI-SINICA, 2019, 34(6): 47-53. doi: 10.7668/hbnxb.20191003.

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