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Acta Agronomica Sinica ›› 2019, Vol. 45 ›› Issue (2): 196-203.doi: 10.3724/SP.J.1006.2019.84100

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

Development and evaluation of InDel markers in cotton based on whole-genome re-sequencing data

Mi WU,Nian WANG,Chao SHEN,Cong HUANG,Tian-Wang WEN,Zhong-Xu LIN()   

  1. National Key Laboratory of Crop Genetic Improvement / College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
  • Received:2018-07-19 Accepted:2018-10-08 Online:2019-02-12 Published:2018-11-16
  • Contact: Zhong-Xu LIN E-mail:linzhongxu@mail.hzau.edu.cn
  • Supported by:
    This study was supported by the Technology Innovation Program of Hubei Province(2018ABA082)

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Abstract:

Insertion and deletion (InDel) are abundant forms of genetic variation in the genome. InDel has been recognized as an ideal source for marker development due to its high-density distribution and genotyping efficiency. In this study, the whole genome re-sequencing data of 262 upland cotton accessions were applied to identify 3206 InDel markers, and 320 markers with uniform distribution across the genome were selected to be evaluated. Eighty-seven polymorphic markers were identified, accounting for 26.88% of screened markers. A total of 160 allelic loci were detected using the 87 polymorphic markers in the 262 upland cotton accessions with an average polymorphic information content (PIC) of 0.3073 (ranging from 0.0836 to 0.3750) and an average genetic diversity of 0.3876 (ranging from 0.0874 to 0.5000), indicating a relatively low genetic diversity. Population structure analysis revealed extensive admixture and identified two subgroups, clustering analysis and principal component analysis supported the subgroups identified by STRUCTURE. Association analysis were performed by MLM (Mixed linear model), and 65 marker loci were associated with fiber quality traits (P < 0.01), explaining 2.57%-8.12% of the phenotypic variation. Genome-wide and gel based InDel markers developed based on re-sequencing data in this study provide a facile tool for cotton germplasm resources research and molecular marker assisted selection breeding.

Key words: Upland cotton, InDel marker, genetic diversity, population structure, association analysis

Fig. 1

Amplification products of marker HAU_ID_D11-01 in some accessions"

Fig. 2

Lines chart of K value with ln P(D) value and ΔK value A: Line chart of ln P(D) value with change of K; B: Line chart of ΔK value with change of K."

Fig. 3

Population structure of 262 upland cotton accessions based on InDel markers"

Fig. 4

PCA plots of 262 upland cotton accessions based on InDel markers NIR: Northwestern Inland Region of China; NSEMR: Northern Specific Early Maturation Region of China; SCR: South China Region; SU: Former Soviet Union; USA: American; YRR: Yellow River Region of China; YtRR: Yangtze River Region of China."

Fig. 5

Phylogenetic tree of the accessions based on genetic distance Red lines: group 1, including 182 accessions; Green lines: group 2, including 80 accessions."

Table 1

Markers associated with multi-traits"

标记位点
Marker locus		 染色体
Chromosome		 位置
Position (bp)		 性状
Trait
HAU_ID_A01-15 A01 93250996 FUHML, FU, SF
HAU_ID_A03-09 A03 57007522 FE, FU, SF
HAU_ID_A08-06 A08 39475602 FE, MV
HAU_ID_A08-07 A08 47285210 FE, MV
HAU_ID_A08-14 A08 98729870 FU, SF
HAU_ID_A09-04 A09 23151235 FUHML, FS
HAU_ID_A10-01 A10 1109653 MV, SF
HAU_ID_A10-09 A10 57152725 FS, FU, MV
HAU_ID_D01-10 D01 43635771 FS, FU
HAU_ID_D02-01 D02 1069504 FUHML, FE
HAU_ID_D02-08 D02 45682280 MV, SF
HAU_ID_D04-07 D04 47451029 FE, MV
HAU_ID_D06-06 D06 35163294 FUHML, FU, SF
HAU_ID_D06-07 D06 39113925 FUHML, FU, SF
HAU_ID_D07-04 D07 23469098 FU, SF
HAU_ID_D07-09 D07 47924875 FUHML, FS, FE, FU, SF
HAU_ID_D09-10 D09 49075327 FUHML, SF
HAU_ID_D11-13 D11 65414930 FE, SF
HAU_ID_D12-10 D12 51191458 FUHML, FS, FU, SF
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