Analysis of genetic differences and construction of an SSR marker fingerprint for Vicia sativa varieties

doi:10.11686/cyxb2018226

Abstract

Abstract: Transcription factors (TFs) are critical adaptor molecules that regulate many plant processes by controlling gene expression. The investigation of the availability of genomics data has proved a valuable resource for TF-SSR markers development. Through the analysis, we developed 208 SSR markers using published transcriptome sequence of Vicia sativa, and 35 pairs of SSR primers were screened out with a high polymorphism, stability, and clear bands. These 35 pairs of SSR primers amplified a total of 288 alleles in 30 V. sativa varieties tested, with an average of 8.23 alleles per SSR marker, the polymorphism ratio (PPB) was 100%, the polymorphic information content (PIC) ranged from 0.42 to 1.00, with an average of 0.80. Six pair of primers with multiple characteristic bands, which together could unambiguously distinguish the 30 tested V. sativa varieties, were selected as the core primers from these 35 pairs of primers. Finally, we constructed the DNA fingerprinting of each of the 30 V. sativa varieties using six core SSR markers. This work established a technical basis for the DUS testing, protection and genetic background analysis of V. sativa.

Key words: Vicia sativa, transcription factors, DUS testing, SSR markers, DNA fingerprinting, genetic differences

MIN Xue-yang, WEI Xing-yi, LIU Wen-xian, ZHANG Zheng-she, JIN Xiao-yu, NDAYAMBAZA Boniface, WU Hong-lin, LI Yu, WANG Yan-rong. Analysis of genetic differences and construction of an SSR marker fingerprint for Vicia sativa varieties[J]. Acta Prataculturae Sinica, 2019, 28(4): 116-128.

References

[1] Upadhyaya H D, Yadav D, Dronavalli N, et al. Mini core germplasm collections for infusing genetic diversity in plant breeding programs. Electronic Journal of Plant Breeding, 2010, 1(4): 1294-1309.
[2] Gowda C L L, Upadhyaya H D, Sharma S, et al. Exploiting genomic resources for efficient conservation and use of chickpea, groundnut, and pigeonpea collections for crop improvement. Plant Genome, 2013, 3(3): 841-856.
[3] Brenner D M, Baltensperger D D, Kulakow P A, et al. Genetic resources and breeding of amaranthus. Plant Breeding Reviews, 2000, 19: 227-285.
[4] Arif I A, Khan H A, Bahkali A H, et al. DNA marker technology for wildlife conservation. Saudi Journal of Biological Sciences, 2011, 18(3): 219-225.
[5] Min X Y, Zhang Z S, Liu Y S, et al. Genome-wide development of microRNA-based SSR markers in Medicago truncatula with their transferability analysis and utilization in related legume species. International Journal of Molecular Sciences, 2017, 18(11): 2440.
[6] Liu W X, Jia X T, Liu Z M, et al. Development and characterization of transcription factor gene-derived microsatellite (TFGM) markers in Medicago truncatula and their transferability in leguminous and non-leguminous species. Molecules, 2015, 20(5): 8759.
[7] Filiz E, Ozdemir B S, Budak F, et al. Molecular, morphological, and cytological analysis of diverse Brachypodium distachyon inbred lines. Genome, 2009, 52(10): 876-890.
[8] Yongjin P, Jukyong L, Namsoo K.Simple sequence repeat polymorphisms (SSRPs) for evaluation of molecular diversity and germplasm classification of minor crops. Molecules, 2009, 14(11): 4546-4569.
[9] Smýkal P, Coyne C J, Ambrose M J, et al. Legume crops phylogeny and genetic diversity for science and breeding. Critical Reviews in Plant Sciences, 2015, 34(1/3): 43-104.
[10] Dong R, Jahufer M, Dong D K, et al. Characterisation of the morphological variation for seed traits among 537 germplasm accessions of common vetch (Vicia sativa L.) using digital image analysis. New Zealand Journal of Agricultural Research, 2016, 59(4): 422-435.
[11] Mo Q, Lü Y Y, Wang Y R.Optimized accelerated aging test for common vetch. Acta Prataculturae Sinica, 2017, 26(11): 131-138.
莫青, 吕燕燕, 王彦荣. 箭筈豌豆种子人工加速老化条件筛选的研究. 草业学报, 2017, 26(11): 131-138.
[12] Niu W, Lu Z J, Zhong M, et al. Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans. Genome Research, 2011, 21(2): 245.
[13] Zhang Z S, Liu W X, Xiao Q, et al. Genome-wide identification, expression profiling, and SSR marker development of the bZIP transcription factor family in Medicago truncatula. Biochemical Systematics & Ecology, 2015, 61: 218-228.
[14] Jin J P, Zhang H, Kong L, et al. PlantTFDB 3.0: A portal for the functional and evolutionary study of plant transcription factors. Nucleic Acids Research, 2014, 42(Database issue): 1182-1187.
[15] Kujur A, Bajaj D, Saxena M S, et al. Functionally relevant microsatellite markers from chickpea transcription factor genes for efficient genotyping applications and trait association mapping. DNA Research, 2013, 20(4): 355-374.
[16] Chai X T, Dong R, Liu W X, et al. Optimizing sample size to assess the genetic diversity in common vetch (Vicia sativa L.) populations using start codon targeted (SCoT) markers. Molecules, 2017, 22(4): 567.
[17] Gupta S, Prasad M.Development and characterization of genic SSR markers in Medicago truncatula and their transferability in Leguminous and non-Leguminous species. Genome, 2009, 52(9): 761.
[18] Conesa A, Götz S, García-Gómez J M, et al. Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 2005, 21(18): 3674-3676.
[19] Ye J, Fang L, Zheng H K, et al. WEGO: A web tool for plotting GO annotations. Nucleic Acids Research, 2006, 34(Web Server issue): W293-W297.
[20] Nei M.Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences of the United States of America, 1973, 70(12): 3321-3323.
[21] Gunjaca J, Buhinicek I, Jukic M, et al. Discriminating maize inbred lines using molecular and DUS data. Euphytica, 2008, 161(1/2): 165-172.
[22] Reid A, Hof L, Felix G, et al. Construction of an integrated microsatellite and key morphological characteristic database of potato varieties on the EU common catalogue. Euphytica, 2011, 182(2): 239-249.
[23] Liu W X, Xiong C H, Yan L F, et al. Transcriptome analyses reveal candidate genes potentially involved in Al stress response in alfalfa. Frontiers in Plantence, 2017, 8: 26.
[24] Liu W X, Zhang Z S, Chen S Y, et al. Global transcriptome profiling analysis reveals insight into saliva-responsive genes in alfalfa. Plant Cell Reports, 2016, 35(3): 561-571.
[25] Min X Y, Liu W X, Zhang Z S, et al. Construction of SSR marker fingerprint database of standard alfalfa varieties utilizing DUS tests. Acta Prataculturae Sinica, 2017, 26(11): 47-56.
闵学阳, 刘文献, 张正社, 等. 苜蓿DUS测试标准品种SSR分子标记指纹图谱的构建. 草业学报, 2017, 26(11): 47-56.
[26] Liu S R, Liu H W, Wu A L, et al. Construction of fingerprinting for tea plant (Camellia sinensis) accessions using new genomic SSR markers. Molecular Breeding, 2017, 37(8): 93.
[27] Shahin Kaleybar B, Kabirnattaj S, Nematzadeh G A, et al. Fingerprinting and genetic diversity evaluation of rice cultivars using Inter Simple Sequence Repeat marker. Journal of Plant Molecular Breeding, 2015, 3(1): 81-91.
[28] Kuang M, Yang W H, Xu H X, et al. Primary construction of a DNA fingerprint database of leading cotton varieties in China. Cotton Science, 2012, 24(3): 229-237.
匡猛, 杨伟华, 许红霞, 等. 中国棉花主栽品种DNA指纹数据库初步构建研究. 棉花学报, 2012, 24(3): 229-237.
[29] Bandelj D, Jakše J, Javornik B.Assessment of genetic variability of olive varieties by microsatellite and AFLP markers. Euphytica, 2004, 136(1): 93-102.
[30] Kim T S, Raveendar S, Suresh S, et al. Transcriptome analysis of two Vicia sativa subspecies: Mining molecular markers to enhance genomic resources for vetch improvement. Genes, 2015, 6(4): 1164-1182.
[31] Chung J W, Kim T S, Sundan S, et al. New cDNA-SSR markers in the narrow-leaved vetch (Vicia sativa subsp. nigra) using 454 pyrosequencing. Molecular Breeding, 2014, 33(3): 749-754.
[32] Liu Z P, Liu P, Luo D, et al. Exploiting illumina sequencing for the development of 95 novel polymorphic EST-SSR markers in common vetch (Vicia sativa subsp. sativa). Molecules, 2014, 19(5): 5777-5789.