Scientia Agricultura Sinica ›› 2020, Vol. 53 ›› Issue (10): 1940-1949.doi: 10.3864/j.issn.0578-1752.2020.10.002

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

Developing SSR Markers of Proso Millet Based on Transcriptome Sequencing

CHEN XiaoHong1,HE JieLi2,SHI TianTian1,SHAO HuanHuan1,WANG HaiGang3,CHEN Ling3,GAO ZhiJun4,WANG RuiYun1,3(),QIAO ZhiJun3()   

  1. 1 College of Agronomy, Shanxi Agricultural University, Taigu 030801, Shanxi
    2 College of Arts and Sciences, Shanxi Agricultural University, Taigu 030801, Shanxi
    3 Institute of Crop Germplasms Resources, Shanxi Academy of Agricultural Sciences/Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture/Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Taiyuan 030031
    4 Erdos Institute of Agriculture and Animal Husbandry, Erdos 017200, Inner Mongolia
  • Received:2019-07-25 Accepted:2020-02-20 Online:2020-05-16 Published:2020-05-22
  • Contact: RuiYun WANG,ZhiJun QIAO E-mail:wry925@126.com;nkypzs@126.com

Abstract:

【Objective】Based on the data of transcriptome sequencing, 200 pairs of SSR primers were detected using six proso millet accessions with different origin. The aim of this study is to construct a set of molecular markers for assessing the genetic diversity of proso millet germplasms.【Method】Primer Premier 5.0 software was used to design primers, DNA was extracted by modified CTAB method and amplified by PCR. Polyacrylamide gel electrophoresis was used to screen the polymorphism of primers. Genetic diversity parameters were calculated with PowerMarker 3.25 and PopGen 1.32.【Result】Ninety seven and eighty out of 200 pairs of primers were shown monomorphic and polymorphic, respectively. A total of 20 were mono-nucleotide SSRs, among them 10 were polymorphic with repeat motif A (50%) and T (50%). A total of 36 were di-nucleotide SSRs, among them 15 were polymorphic with seven types of repeat motif, AG class was the most frequent, followed by the TC, GC and GA, CA, TA and AC were the least. A total of 144 were tri-nucleotide SSRs, among them 55 were polymorphic with 24 types of repeat motif, GGC, GCG and GCC class were the most frequent, followed by the GAA, GCT, CGC, etc, ACC, AGG, CAG, CGT, AAG, AAC, TCG, CGA, ATT, CAA and CCA were the least. In terms of the mono-, di-, tri-nucleotide SSR, their Rp value ranged from 0.67 to 4.67 (mean 2.07), 1.33 to 4.33 (mean 2.73) and 0.67 to 4.00 (mean 1.83), respectively. Evaluating the distribution frequency based on Rp, 80 SSRs were divided into five intervals viz 0-1, 1-2, 2-3, 3-4 and 4-5, with 17 (21.25%), 36 (45.00%), 11 (13.75%), 14 (17.50%) and 2 (2.50%) markers, respectively. For the mean of the Rp value, the mono-, di-, tri-nucleotide SSR were 0.33 to 0.67 (average 0.51), 0.40 to 0.78 (average 0.59) and 0.33 to 0.83 (average 0.59), respectively. As for mono-nucleotide SSRs, a total of 22 allelic variations were detected with 2-3 alleles (average 2.2000) for each locus; 2 and 3 alleles were identified for 8 and 2 loci, respectively. In terms of di-nucleotide SSRs, a total of 38 allelic variations were generated with 2-3 alleles (average 2.5333) for each locus; 7 and 8 loci produced 2 and 3 alleles, respectively. As for tri-nucleotide SSRs, a total of 136 allelic variations were generated with 2-3 alleles (average 2.4727) for each locus; 29 and 26 loci produced 2 and 3 alleles, respectively. In terms of the polymorphism information content, the mono-, di-, tri-nucleotide SSR were 0.3750-0.5355, 0.2392-0.7438 and 0.2392-0.7438, respectively. In terms of the diversity index, the mono-, di-, tri-nucleotide SSR were 0.6365-1.0776 (average 0.7497), 0.5623-1.0986 (average 0.8339) and 0.5623-1.0889 (average 0.8312), respectively. 【Conclusion】Two hundreds pairs of SSR primers obtained from transcriptome sequencing were used to detect genetic diversity of 6 proso millet accessions. It was shown that 177 (88.5%) out of the 200 pairs primers amplified intact bands, and 80 SSRs appeared polymorphic with the polymorphic rate 40%.

Key words: proso millet (Panicum miliaceun L.), SSR, resolving power (Rp), polymorphism information content (PIC), diversity index

Table 1

Proso millet accessions for screening SSR primers"

序号 No. 统一编号 Unicode 名称 Accession name 来源 Origin 生态栽培区 Ecotope
1 00000177 红糜子Hongmizi 黑龙江省宁安市
Ning’an, Heilongjiang
东北春糜子区
Northeast spring-sowing ecotope
2 00000750 白糜子Baimizi 新疆沙湾县
Shawan, Xinjiang
西北春夏糜子区
Northwest spring & summer-sowing ecotope
3 00006653 金黍Jinshu 海南省
Hainan
南方秋冬糜子区
Southern autumn & winter-sowing ecotope
4 00007238 大红糜子Dahongmizi 内蒙古巴彦淖尔
Bayanzhuoer, Inner Mongolia
北方春糜子区
Northern spring-sowing ecotope
5 00007478 白圪塔糜Baigetami 青海省湟中县
Huangzhong, Qinghai
西北春夏糜子区
Northwest spring & summer-sowing ecotope
6 红黍子Hongshuzi 河南省安阳市
Anyang, Henan
华北夏糜子区
Northern summer-sowing ecotope

Fig. 1

Genetic DNA bands running through agarose gel electrophoresis"

Fig. 2

Repeat motif distribution of 200 pairs of primer"

Fig. 3

Type and distribution of mono-nucleotide motif SSR"

Fig. 4

Type and distribution of di-nucleotide motif SSR"

Fig. 5

Type and distribution of tri-nucleotide motif SSR"

Fig. 6

Resolving power values of 80 SSR marker in proso millet"

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