JIA-2022-0131 全基因组水平开发甘蔗高贵种与割手密种的种间微卫星分子标记

doi:10.1016/j.jia.2022.08.129

Journal of Integrative Agriculture ›› 2022, Vol. 21 ›› Issue (11): 3230-3244.DOI: 10.1016/j.jia.2022.08.129

JIA-2022-0131 全基因组水平开发甘蔗高贵种与割手密种的种间微卫星分子标记

收稿日期:2022-01-28 接受日期:2022-07-14 出版日期:2022-11-01 发布日期:2022-07-14

Genome-wide development of interspecific microsatellite markers for Saccharum officinarum and Saccharum spontaneum

LIU Lei¹, WANG Heng-bo¹, LI Yi-han^1,2, CHEN Shu-qi¹, WU Ming-xing¹, DOU Mei-jie¹, QI Yi-yin¹, FANG Jing-ping³, ZHANG Ji-sen^1,2

¹Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, P.R.China

²State Key Lab for Conservation and Utilization of Subtropical Agro-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530004, P.R.China
³College of Life Sciences, Fujian Normal University, Fuzhou 350007, P.R.China

Received:2022-01-28 Accepted:2022-07-14 Online:2022-11-01 Published:2022-07-14
About author:Correspondence FANG Jing-ping, E-mail:jinphia@163.com; ZHANG Ji-sen, E-mail: zjisen@126.com
Supported by:
This work was supported by the National Key Research and Development Program of China (2021YFF1000101-5), the Science and Technology Planting Project of Guangdong Province, China (2019B020238001), the Natural Science Foundation of Fujian Province, China (2019J05066), the National Natural Science Foundation of China (41906096), and the Guangdong Laboratory for Lingnan Modern Agriculture and the State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, China.

摘要/Abstract

摘要：

甘蔗具有庞大、复杂的多倍体基因组，阻碍了其基因组学和分子标记辅助选择的研究进展。简便易用的微卫星分子标记（SSR）因其理想的遗传属性而备受关注，但由于此前缺乏高质量染色体水平的甘蔗基因组，这些标记尚未在甘蔗全基因组范围内进行开发。本研究从甘蔗高贵种和割手密种基因组中鉴定到744,305和361,638个候选SSRs。为验证这些预测SSR的可靠性，使用11份代表性甘蔗材料（包括高贵种、割手密种、大茎野生种和现代栽培种）对1,200对种间特异SSR引物的多态性进行检测。结果表明，共有660对SSR标记在这些材料中呈现为种间多态性。此外，随机选取了100对SSR标记，对39份具有代表性的甘蔗材料进行遗传多样性分析。利用100条多态性引物共获得320个等位位点，每对SSR标记的等位位点为2-7个。遗传多样性分析结果表明，这些种质资源主要分布在4个类群中，分别为I类(14份割手密种)、II类(2份高贵种)、III类(18份现代甘蔗杂交种)和IV类(5份大茎野生种)。实验结果证明了本研究中基于甘蔗基因组预测所获得的SSR分子标记的可靠性。基于实验验证的大量SSR分子标记的开发对甘蔗遗传连锁图谱构建、比较基因组分析、全基因组关联分析和分子标记辅助选择等遗传研究具有重要意义。

Abstract:

Sugarcane has a large, complex, polyploid genome that has hindered the progress of genomic research and molecular marker-assisted selection. The user-friendly SSR markers have attracted considerable attention owing to their ideal genetic attributes. However, these markers were not characterized and developed at the genome-wide scale due to the previously lacking high-quality chromosome-level assembled sugarcane genomes. In this present study, 744 305 and 361 638 candidate SSRs were identified from the genomes of S. officinarum and S. spontaneum, respectively. We verified the reliability of the predicted SSRs by using 1 200 interspecific SSR primer pairs to detect polymorphisms among 11 representative accessions of Saccharum, including S. spontaneum, S. officinarum, S. robustum, and modern sugarcane hybrid. The results showed that 660 SSR markers displayed interspecific polymorphisms among these accessions. Furthermore, 100 SSRs were randomly selected to detect the genetic diversity for 39 representative Saccharum accessions. A total of 320 alleles were generated using 100 polymorphic primers, with each marker ranging from two to seven alleles. The genetic diversity analysis revealed that these accessions were distributed in four main groups, including group I (14 S. spontaneum accessions), group II (two S. officinarum accessions), group III (18 modern sugarcane hybrid accessions), and group IV (five S. robustum accessions). Experimental verification supported the reliability of the SSR markers based on genome-wide predictions. The development of a large number of SSR markers based on wet experiments is valuable for genetic studies, including genetic linkage maps, comparative genome analysis, genome-wide association studies, and marker-assisted selection in Saccharum.

Key words: Saccharum , genome-wide , simple repeat sequences (SSR) , microsatellite , molecular markers

. JIA-2022-0131 全基因组水平开发甘蔗高贵种与割手密种的种间微卫星分子标记[J]. Journal of Integrative Agriculture, 2022, 21(11): 3230-3244.

LIU Lei, WANG Heng-bo, LI Yi-han, CHEN Shu-qi, WU Ming-xing, DOU Mei-jie, QI Yi-yin, FANG Jing-ping, ZHANG Ji-sen. Genome-wide development of interspecific microsatellite markers for Saccharum officinarum and Saccharum spontaneum[J]. Journal of Integrative Agriculture, 2022, 21(11): 3230-3244.

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JIA-2022-0131 全基因组水平开发甘蔗高贵种与割手密种的种间微卫星分子标记

Genome-wide development of interspecific microsatellite markers for Saccharum officinarum and Saccharum spontaneum

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