南酸枣转录组特征分析及SSR标记开发

徐梦阳<sup>1; 2</sup>; 蔡宇宇<sup>1; 2</sup>; 李 婷<sup>1; 2</sup>; 吴南生<sup>1; 2</sup>; 孙荣喜<sup>1; 2*</sup>

引用本文:	徐梦阳, 蔡宇宇, 李婷, 吴南生, 孙荣喜.南酸枣转录组特征分析及SSR标记开发[J].广西植物,2025,45(4):641-653.[点击复制]
	XU Mengyang, CAI Yuyu, LI Ting, WU Nansheng, SUN Rongxi.Transcriptome characteristic analysis and SSR marker development of Choerospondias axillaris[J].Guihaia,2025,45(4):641-653.[点击复制]

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南酸枣转录组特征分析及SSR标记开发
徐梦阳^1,2, 蔡宇宇^1,2, 李婷^1,2, 吴南生^1,2, 孙荣喜^1,2*
1. 江西农业大学林学院南酸枣研究所, 南昌 330045;2. 江西农业大学林学院亚热带森林资源培育江西省重点实验室, 南昌 330045

摘要:

通过对南酸枣(Choerospondias axillaris)雌雄转录组特征分析及SSR标记开发,为其遗传评价和性别分子辅助育种提供理论支撑和科学依据。该文主要分析南酸枣雌雄转录组表达差异,SSR位点的分布及序列特征,在此基础上开展SSR位点挖掘,并进行SSR引物的开发和有效性验证。结果表明:(1)南酸枣转录组测序共获得40 341条Unigenes序列,总长度、N50长度、平均长度和GC含量分别为52 806 369 bp、2 409 bp、1 309 bp和38.75%; 共筛选到1 949个雌雄差异表达基因,其中雄株比雌株显著上调的基因有1 052 个,下调的基因有897 个。(2)在所有Unigenes中共检测到5 251个SSR位点,619条Unigenes序列中含有2个及2个以上位点,SSR发生频率为11.18%,平均分布距离为10.06 kb; 在所有SSR位点中,二核苷酸重复所占比例最高(46.95%),其次为三核苷酸重复(34.27%)。(3)经筛选及有效性验证共得到20对SSR多态性引物,在85份资源中共检测到80个等位基因,平均多态性信息含量(PIC)为0.56。综上认为,南酸枣叶片转录组测序质量较高,组装效果较好。20对多态性引物为后期遗传评价、性别辅助育种及指纹图谱构建提供参考。

关键词: 南酸枣, 引物开发, 转录组, SSR, 位点特征

DOI：10.11931/guihaia.gxzw202406022

分类号:Q943

文章编号:1000-3142(2025)04-0641-13

基金项目:国家自然科学基金(32160387)。

Transcriptome characteristic analysis and SSR marker development of Choerospondias axillaris

XU Mengyang^1,2, CAI Yuyu^1,2, LI Ting^1,2, WU Nansheng^1,2, SUN Rongxi^1,2*

1. Institute of Choerospondias axillaris Research, College of Forestry, Jiangxi Agricultural University, Nanchang 330045, China;2. Jiangxi Provincial Key Laboratory of Subtropical Forest Resources Cultivation, College of Forestry, Jiangxi Agricultural University, Nanchang 330045, China 1. Institute of Choerospondias axillaris Research, College of Forestry, Jiangxi Agricultural University, Nanchang 330045, China; 2. Jiangxi Provincial Key Laboratory of Subtropical Forest Resources Cultivation, College of Forestry, Jiangxi Agricultural University, Nanchang 330045, China

Abstract:

Transcriptome characteristic analysis and SSR marker was developed based on the leaf transcriptome sequences of Choerospondias axillaris in order to provide theoretical support and scientific basis for genetic evaluation, and sex marker-assisted breeding of C. axillaris. Differential expression of male and female transcriptomes, the distribution and sequence characteristics of SSR locus were analyzed, and SSR locus mining, development and validation were conducted based on the transcriptome data. The results were as follows:(1)A total of 40 341 Unigenes sequences were obtained from male and female transcriptomes of C. axillaris. The total length, the length of N50, average length and GC content were 52 806 369 bp, 2 409 bp, 1 309 bp, and 38.75%, respectively. A total of 1 949 differentially expressed genes between males and females were screened, among them, 1 052 genes were significantly upregulated and 897 genes were downregulated in male compared to female.(2)Among all Unigenes, 5 251 SSR loci were detected with 619 Unigenes sequences containing two or more SSR loci, resulting in an SSR occurrence frequency of 11.18% and an average distribution distance of 10.06 kb. Among all SSR loci, dinucleotide repeats accounted for the highest proportion(46.95%), followed by trinucleotide repeats(34.27%).(3)A total of 20 pairs of SSR polymorphic primers were obtained through screening and validation, detecting 80 alleles among 85 samples, with an average polymorphism information content(PIC)of 0.56. In summary, the sequencing quality of C. axillaris is high, and the assembly effect is good. The 20 pairs of primers is found that had high suitability, which can provide reference for the analysis of population genetic diversity, sex marker-assisted breeding and fingerprints construction of C. axillaris.

Key words: Choerospondias axillaris, primer development, transcriptome, SSR, locus characteristics