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Acta Agronomica Sinica ›› 2018, Vol. 44 ›› Issue (9): 1400-1410.doi: 10.3724/SP.J.1006.2018.01400

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Development and Characterization of SSR Markers from the Whole Genome Sequences of Saccharum officinarum (LA-purple)

Heng-Bo WANG(),Nai-Yan XIAO,Zhuan-Wei ZHU,Cui-Cui LIU,ALAM Intikhab,Ping-Hua CHEN,Yun-Hai LU()   

  1. Key Laboratory of Ministry of Agriculture for Sugarcane Biology and Genetic Breeding (Fujian), Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
  • Received:2017-11-20 Accepted:2018-03-26 Online:2018-09-10 Published:2018-04-09
  • Contact: Yun-Hai LU E-mail:wanghengbo_0354@126.com;lu@fafu.edu.cn
  • Supported by:
    This study was supported by the China Agriculture Research System(CARS-20-1);National Sugarcane Engineering Research Center of Director Project Fund in 2017 (ptjh1500117)

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Abstract:

Modern sugarcane cultivars (2n = 100-130) are derived from interspecific hybridization and backcross breeding between Saccharum officinarum (2n = 80) and Saccharum spontaneum (2n = 40-128), forming polyploid and aneuploid crops. The main components (80%-90%) of the sugarcane cultivars’ genome are originated from S. officinarum. The development and mining of genomic SSR molecular marker of S. officinarum, will benefit sugarcane genetic diversity analysis, molecular marker assisted selection, and construction of genetic maps. In this study, we explored the SSR loci from 255 398 predicted gene sequences (with a cumulative length of 1 029 222 285 bp) derived from the whole genome sequencing project of a S. officinarum clone LA-purple, by combining Perl program with bioinformatics software. A total of 153 150 SSR loci, with an average of 1.67 genes per SSR locus, were identified, of which 39 556 (25.8%) were dinucleotide repeat motifs and 50 072 (32.7%) were tri-nucleotide repeat motifs. Among the dinucleotide repeat motifs, TA/AT had the highest proportion, accounting for 41.4%, while CG/GC had the lowest proportion, accounting for only 4.6%. Among the trinucleotide repeat motifs, TGT/ACA had the highest proportion, accounting for 15.6%. One hundred SSR loci with 60-90 repeats of TA/AT motifs were selected and analyzed by PCR amplification in 12 representative Saccharum clones, of which 52 were polymorphic among the 12 clones and 27 were polymorphic between the tested two modern sugarcane cultivars. The genome-wide development of these gene-based SSR markers will not only facilitate the DNA fingerprinting analysis of sugarcane cultivars, but also help to construct the genetic maps, analyze the genetic diversity, study the genetic mechanism of important traits in Saccharum species, and provide important support to the molecular breeding in sugarcane.

Key words: sugarcane, genome sequence, SSR, marker development, polymorphism

Table 1

Names and origins of sugarcane germplasm used in the experiment"

序号
Code		 名称
Name		 类型
Type		 倍性
Ploidy
1 57NG208 大茎野生种 S. robustum
2 NG77-004 大茎野生种 S. robustum
3 云南75-2-11 YN75-2-11 割手密 S. spontaneum 八倍体 Octoploid
4 福建89-1-1 FJ89-1-1 割手密 S. spontaneum 九倍体 Nonaploid
5 广东21 GD21 割手密 S. spontaneum 十倍体 Decaploid
6 贵州78-2-28 GZ78-2-28 割手密 S. spontaneum 十二倍体 Dodecaploid
7 黑车里本 Black cheribon 热带种 S. officinarum 八倍体 Octoploid
8 路达士 Loethers 热带种 S. officinarum 八倍体 Octoploid
9 克里斯塔林娜 Crystalina 热带种 S. officinarum 八倍体 Octoploid
10 拔地拉 Badila 热带种 S. officinarum 八倍体 Octoploid
11 桂糖35 GT35 栽培种 Saccharun hybrid
12 科5 K5 栽培种 Saccharun hybrid

"

Fig. 1

Frequency distribution of dinucleotide repeat motifs"

Fig. 2

Frequency distribution of trinucleotide repeat motifs"

Fig. 3

Representative PCR amplification patterns of four pairs of SSR primers of AT/TA motif in 12 tested Saccharum clones1: 57NG208; 2: NG77-004; 3: YN75-2-11; 4: FJ89-1-1; 5: GD21; 6: GZ78-2-28; 7: Black cheribon; 8: Loethers; 9: Crystalina; 10: Badila; 11: GT35; 12: K5; M: 100 bp DNA ladder."

"

Fig. 4

UPGMA dendrogram of 12 Saccharum clones based on SSR markers"

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