摘要
【目的】目前杉木分子标记数量无法满足种质资源评价及分子标记辅助育种等相关研究需求,需要开发更多的杉木SSR标记十分重要。【方法】以陈山红心杉转录组测序数据为基础,进行EST-SSR标记的检测和开发,并对陈山红心杉二代种子园进行遗传变异分析。【结果】转录组测序共获得99 122 394个reads片段,包含了14.87 Gb的序列数据。序列组装后,获得76 597个unigene,共计104.18 Mb数据,平均长983 bp。寻找到8 072个SSR位点,单核苷酸和三核苷酸是主要重复类型,分别占总数的66.30%和17.48%,其次是二核苷酸重复类型,占总数的12.31%。AT/TA和AG/TC是主要的双碱基重复序列,分别占总位点数的6.79%和1.93%。AGA/TCT和AAG/TTC是主要的三碱基重复序列,分别占总位点数的1.45%和1.44%。从随机挑选的150对SSR引物中筛选出11对多态性引物。陈山红心杉二代种子园SSR位点间的平均等位基因数为4.4个,有效等位基因为2.4个;群体平均观察杂合度、期望杂合度、Shannon多样性指数分别为0.533 5、0.563 8、1.003 4,表明该种子园遗传多样性较高。陈山红心杉二代种子园无性系间的遗传相似系数在0.240 0~0.977 8之间,平均值为0.589 3,说明这一群体有较宽的遗传基础。在阈值0.62处可将无性系划分为6个亚群体,亚群体内个体数量差异较大。【结论】本研究基于陈山红心杉转录组数据开发出11对EST-SSR标记,丰富了杉木分子标记库,这些标记可用于杉木种质资源评价、遗传多样性分析及分子标记辅助育种等方面。
【Objective】At present, the available molecular markers of Chinese fir are deficient, which can not meet the needs of molecular marker assisted breeding and evaluation of germplasm resources. It’s quite important to develop more reliable SSR markers for Chinese fir.【Method】In this study, transcriptome data of chenshan red-heart Chinese fir were used as materials to develop and verify EST-SSR markers. Moreover, the genetic diversity for a second generation clonal seed orchard of Red-heart Chinese fir was analyzed by using 14 SSR markers.【Result】The results show that 99 122 394 reads containing 14.87 Gb in sequence information are generated. A total of 76 597 unigenes containing 104.18 Mb in sequence information are formed by initial sequence splicing,with an average read length of 983 bp. 8 072 repeat contigs containing SSR are found by MISA software. Mononucleotide and trinucleotide are the dominant repetitive sequences in SSR loci, which account for 66.30% and 17.48%, respectively, followed by the dinucleotide with 12.31%. AT/TA(6.79%) and AG/TC(1.93%) are the dominant dinucleotide repeat motifs, AGA/TCT(1.45%) and AAG/TTC(1.44%) are the dominant trinucleotide repeat motifs. 150 pairs of primer are randomly selected for PCR amplification. Among them, 11 pairs of primers are amplified with clear bands, which have good polymorphism and repeatability. These EST-SSR markers and three other ESTSSR markers are used to detect genetic diversity for the second generation clone seed orchard of Red-heart Chinese fir. The average number of alleles and effective alleles per locus are 4.4 and 2.4, respectively. The expected heterozygosity, observed heterozygosity and shannon’s information index are 0.533 5, 0.563 8 and 1.003 4, respectively. The average genetic similarity coefficients between clones range from 0.240 0 to 0.977 8 with an average of 0.589 3, indicating that this seed orchard has a wide genetic basis. According to the genetic similarity of 0.62, the samples are divided into 6 subgroups by UPGMA cl
作者
陈兴彬
何龙燕
肖复明
娄永峰
徐海宁
孙世武
CHEN Xingbin;HE Longyan;XIAO Fuming;LOU Yongfeng;XU Haining;SUN Shiwu(Jiangxi Provincial Key Lab for Plant Biotechnology,Jiangxi Academy of Forestry,Nanchang 330013,Jiangxi,China;Xiamen Jiangping Biotechnology Co.,Ltd,Xiamen 361000,Fujian,China;Baiyun Mountain Forest Farm of Qingyuan District,Ji’an 343000,Jiangxi,China)
出处
《中南林业科技大学学报》
CAS
CSCD
北大核心
2020年第8期120-127,共8页
Journal of Central South University of Forestry & Technology
基金
江西省重点研发计划项目(20181ACF60011)
江西省林业科技创新项目(201802)
江西省林业科学院博士启动项目(2017521101)
江西省林业科学院青年科技人才培养项目(2018521101)。
关键词
陈山红心杉
SSR
转录组
标记开发
chenshan red-heart Chinese fir
SSR
transcriptome
marker development
