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Molecular characterization of sweet potato(Ipomoea batatas[L.]Lam)germplasms for desirable traits by using simple sequence repeats markers
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作者 KHANDAKAR ABUMDMOSTAFIZAR RAHMAN ABDUL SHUKOR JURAIMI +6 位作者 MDREZWAN MOLLA MUHAMMAD ASYRAFMD HATTA ZULKEFLY BIN SULAIMAN SHAMIMA SULTANA AHMED GABER BENUKAR BISWAS AKBAR HOSSAIN 《BIOCELL》 SCIE 2023年第1期227-237,共11页
Every breeding program that aims to create new and improved cultivars with desired traits mostly relies on information related to genetic diversity.Therefore,molecular characterization of germplasms is important to ob... Every breeding program that aims to create new and improved cultivars with desired traits mostly relies on information related to genetic diversity.Therefore,molecular characterization of germplasms is important to obtain target cultivars with desirable traits.Sweet potato[Ipomoea batatas(L.)Lam]is widely considered the world’s most important crop,with great diversity in morphological and phenotypic traits.The genetic diversity of 20 sweet potato germplasms originating from Bangladesh,CIP,Philippines,Taiwan,and Malaysia were compared,which was accomplished by genetic diversity analysis by exploring 20 microsatellite DNA markers for germplasm characterization and utilization.This information was effective in differentiating or clustering the sweet potato genotypes.A total of 64 alleles were generated using the 20 primers throughout the 20 germplasm samples,with locus IBS97 having the highest number of alleles(5),whereas locus IbU33 had the fewest alleles(2).The alleles varied in size from 105(IbU31)to 213 base pairs(IBS34).The Polymorphism Information Content(PIC)values for the loci IbL46 and IBS97 varied from 0.445 to 0.730.IBS97 has the highest number of effective alleles(3.704),compared to an average of 2.520.The average Shannon’s diversity index(H)was 1.003,ranging from 0.673 in IbU3 to 1.432 in IBS97.The value of gene flow(Nm)varied between 0.000 and 0.005,with an average of 0.003,whereas genetic differentiation(FST-values)ranged between 0.901 and 1.000.The sweet potato germplasm included in this study had a broad genetic base.SP1 vs.SP9 and SP12 vs.SP18 germplasm pairings had the greatest genetic distance(GD=0.965),while SP1 vs.SP2 germplasm couples had the least genetic diversity(GD=0.093).Twenty genotypes were classified into two groups in the UPGMA dendrogram,with 16 genotypes classified as group“A”and the remaining four genotypes,SP10,SP18,SP19,and SP20,classified as group“B.”According to cluster analysis,the anticipated heterozygosity(gene diversity)of Nei(1973)was 0.591 on average.In summary,SSR markers successfully evaluated the genetic relationships among the sweet potato accessions used and generated a high level of polymorphism.The results of the present study will be useful for the management of germplasm,improvement of the current breeding strategies,and the release of new cultivars as varieties. 展开更多
关键词 Sweet potato simple sequence repeats(ssrs) Genetic diversity DENDROGRAM
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High-throughput simple sequence repeat (SSR) markers development for the kelp grouper (<i>Epinephelus bruneus</i>) and cross-species amplifications for Epinephelinae species 被引量:2
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作者 Satoshi Kubota Qi Liu +9 位作者 Kanonkporn Kessuwan Nobuaki Okamoto Takashi Sakamoto Yoji Nakamura Yuya Shigenobu Takuma Sugaya Motohiko Sano Susumu Uji Kazuharu Nomura Akiyuki Ozaki 《Advances in Bioscience and Biotechnology》 2014年第2期117-130,共14页
The kelp grouper (Epinephelus bruneus), belonging to one of the largest genera among the subfamily Epinephelinae, is a commercially important fish in Japan. There are limited data about the genomics of this species. T... The kelp grouper (Epinephelus bruneus), belonging to one of the largest genera among the subfamily Epinephelinae, is a commercially important fish in Japan. There are limited data about the genomics of this species. To provide tools for addressing both population genetics studies and gene mapping, dito pentanucleotide simple sequence repeat (SSR) markers were developed using 454 pyrosequencing. Among the 1466 SSR markers developed, 1244 primer sets produced strong PCR products, of which 905 (72.7%) were polymorphic in kelp grouper. Cross-species utility of the 905 polymorphic SSR markers was tested in four additional Epinephelinae species of Hyporthodus septemfasciatus, Plectropomus leopardus, Epinephelus lanceolatus and Epinephelus coioides. Results revealed that, respectively, 401 (44.3%), 136 (15.0%), 434 (49.0%) and 538 (59.4%) SSRs showed specific polymorphic products. Of these, 40 SSR markers (33 di-, 1 tri- and 6 tetra-nucleotides) showed polymorphism in all species tested. Additionally, three AGAT SSR motifs which accounted for 42.9% of the nondi-nucleotide markers were found in the 40 SSR markers. This indicates that the AGAT SSR motif has a high potential as a highly versatile SSR marker in grouper Epinephelinae. The SSR markers developed in this study can be employed to obtain reliable genetic variability estimates for groupers (Epinephelinae). 展开更多
关键词 KELP GROUPER EPINEPHELUS bruneus repeat Motif simple sequence repeat (ssr) 454 Pyrosequencing Cross-Species Amplification
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Confirmation of Pearl Millet-Napiergrass Hybrids Using EST-Derived Simple Sequence Repeat (SSR) Markers
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作者 Charlie D. Dowling Byron L. Burson +2 位作者 Jamie L. Foster Lee Tarpley Russell W. Jessup 《American Journal of Plant Sciences》 2013年第5期1004-1012,共9页
Prospects for deploying perennial grasses that are currently considered leading candidates for dedicated energy crops over large acreages are debatable because of several limitations, including vegetative propagation ... Prospects for deploying perennial grasses that are currently considered leading candidates for dedicated energy crops over large acreages are debatable because of several limitations, including vegetative propagation or small seed size, low biomass production during the first growing season, and incomplete assessments of crop invasiveness risk. Pearl Millet-Napiergrass hybrids (“PMN”;Pennisetum glaucum [L.] R. Br. × P. purpureum Schumach.), in contrast, are large-seeded, sterile feedstocks capable of high biomass production during establishment year. Novel methods are warranted for confirmation of PMN hybrids, as traditional morphological observations can be inconclusive and chromosome number determination using cytological methods is laborious and time consuming. Six putative PMN lines were produced in this study, and 10 progeny from each line were evaluated using morphological traits, seed fertility, flow cytometry, and expressed sequence tag-simple sequence repeat (EST-SSR) markers. All putative hybrid lines were sterile and failed to produce seed. The PMN hybrids could not be distinguished from either parent using flow cytometry due to highly similar nuclear genome DNA contents. A number of paternal napiergrass-specific EST-SSRs were identified for each PMN line, and four paternal-specific EST-SSRs conserved across all napiergrass accessions were selected to screen the putative PMN hybrids. These EST-SSRs confirmed that all F1 individuals analyzed were PMN hybrids. The use of paternal-specific markers therefore provides a valuable tool in the development of both “Seeded-yet-Sterile” biofuel PMN feedstocks and additional PMN cultivar-and parental species-specific markers. 展开更多
关键词 PENNISETUM glaucum PENNISETUM purpureum Bulked Segregant Analysis marker-Assisted Selection marker-Assisted Breeding EST-ssr Expressed sequence Tag simple sequence repeat Microsatellites Biofuel Biofuels PEARL MILLET × NAPIERGRASS PEARL MILLET NAPIERGRASS INTERSPECIFIC Hybrid PCR Polymerase Chain Reaction Comparative Genomics
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油菜简单重复序列SSR(simple sequence repeat)研究进展 被引量:19
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作者 刘列钊 林呐 《生命科学》 CSCD 2004年第3期173-176,共4页
简单重复序列(simple sequence repeat, SSR)是重复单元少于6个核苷酸重复序列,广泛分布于动植物基因组中,呈孟德尔遗传,已被作为一种理想的共显性标记应用于动植物遗传研究中。本文重点介绍了SSR分类、特点,及近几年来油菜SSR标记的开... 简单重复序列(simple sequence repeat, SSR)是重复单元少于6个核苷酸重复序列,广泛分布于动植物基因组中,呈孟德尔遗传,已被作为一种理想的共显性标记应用于动植物遗传研究中。本文重点介绍了SSR分类、特点,及近几年来油菜SSR标记的开发和SSR技术在油菜基因定位、品种鉴定中的应用,并对SSR标记在油菜中的应用进行了探讨。 展开更多
关键词 简单重复序列 分子标记 油菜
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Haplotyping of Rice Genotypes Using Simple Sequence Repeat Markers Associated with Salt Tolerance 被引量:3
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作者 A.D.CHOWDHURY G.HARITHA +5 位作者 T.SUNITHA S.L.KRISHNAMURTHY B.DIVYA G.PADMAVATHI T.RAM N.SARLA 《Rice science》 SCIE CSCD 2016年第6期317-325,共9页
Salt stress is a major problem in most of the rice growing areas in the world. A major QTLSaltol associated with salt tolerance at the seedling stage has been mapped on chromosome 1 in rice.This study aimed to charact... Salt stress is a major problem in most of the rice growing areas in the world. A major QTLSaltol associated with salt tolerance at the seedling stage has been mapped on chromosome 1 in rice.This study aimed to characterize the haplotype diversity at Saltol and additional QTLs associated withsalt tolerance. Salt tolerance at the seedling stage was assessed in 54 rice genotypes in the scale of 1to 9 score at EC = 10 dSm^-1 under controlled environmental conditions. Seven new breeding linesincluding three KMR3/O. rufipogon introgression lines showed similar salt tolerant ability as FL478 andcan be good sources of new genes/alleles for salt tolerance. Simple sequence repeat (SSR) markerRM289 showed only two alleles and RM8094 showed seven alleles. Polymorphic information contentvalue varied from 0.55 for RM289 to 0.99 for RM8094 and RM493. Based on 14 SSR markers, the 54lines were clearly separated into two major clusters. Fourteen haplotypes were identified based onSaltol linked markers with FL478 as the reference. Alleles of RM8094 and RM3412 can discriminatebetween the salt tolerant and susceptible genotypes clearly and hence can be useful in marker-assistedselection at the seedling stage. Other markers RM10720 on chromosome 1 and RM149 and RM264 onchromosome 8 can also distinguish tolerant and susceptible lines but with lesser stringency. 展开更多
关键词 HAPLOTYPE rice salt tolerance Saltol simple sequence repeat marker
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Development of Starfruit Simple Sequence Repeat (SSR) Using Next Generation Sequencing
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作者 Khairun Hisam Nasir Muhammad Fairuz Mohd Yusof +5 位作者 Mohd Shahril Firdaus Siti Zainab Jantan Mira Farzana Mohamad Moktar Siti Norsaidah Ibrahim Noor Baiti Abdul Aziz Joanna Cho Lee Ying 《Journal of Food Science and Engineering》 2019年第3期95-121,共27页
Starfruit (Averrhoa carambola L.) is an important fruit for Malaysian export and great attention has been made to improve starfruit fruit quality at Malaysian Agricultural Research and Development Institute (MARDI). T... Starfruit (Averrhoa carambola L.) is an important fruit for Malaysian export and great attention has been made to improve starfruit fruit quality at Malaysian Agricultural Research and Development Institute (MARDI). The current study used next generation sequencing (NGS) technologies to develop starfruit simple sequence repeat (SSR) from 2 varieties namely B11 and B17 using Illumina HiSeq. The pre-processed reads were de novo assembled to generate approximately 75,000 and 74,000 scaffolds respectively. Total genome size for B11 and B17 were around 345 Mbp and 342 Mbp based on K-mer distribution analysis. In-silico microsatellite mining of each variety has identified more than 17,000 SSR in B11 and B17 respectively. Dinucleotides were the most abundant, accounting for more than 70% of all SSR and repeat motif GA (49%) was most common. A total of 239 SSR primer pairs were designed from contigs larger than 350 nucleotides and tested for amplification. The 30 polymorphic SSRs were used to DNA fingerprint of 12 starfruit hybrids. Polymorphism information content (PIC) ranged from 0.1411 to 0.6838, with an average of 0.3919. The Unweighted Pair-Group Method for Arithmetic Averages (UPGMA) dendrogram clustered 12 starfruit accessions into 2 groups. 展开更多
关键词 Starfruit (Averrhoa CARAMBOLA L.) NEXT generation sequencING molecular marker simple sequence repeat
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Full-length transcriptome sequence and SSR marker development for genetic diversity research in yellowfin seabream Acanthopagrus latus
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作者 Jin ZHANG Jinmei LIU +6 位作者 Chong HAN Cheng PENG Yong LI Junhong XIA Yong ZHANG Shuisheng LI Haoran LIN 《Journal of Oceanology and Limnology》 SCIE CAS CSCD 2023年第3期1073-1083,共11页
Yellowfin seabream Acanthopagrus latus is an important economic fish in Chinese coastal areas.Given its narrow distribution and overfishing,the genetic diversity of yellowfin seabream has been restricted for artificia... Yellowfin seabream Acanthopagrus latus is an important economic fish in Chinese coastal areas.Given its narrow distribution and overfishing,the genetic diversity of yellowfin seabream has been restricted for artificial breeding and reproduction.We performed full-length transcriptome sequencing and assembly of the genome of yellowfin seabream.A total of 68086 unigenes were obtained,with an N50 of 3391 bp on average length of 2933 bp.A total number of 50593 expressed sequence tags linked to simple sequence repeats(EST-SSR)were identified,among them dinucleotide repeats(40.6%)and AC/GT motifs(38.5%)were the most frequent.Of the 190 EST-SSRs for which PCR primer pairs were designed,150 primer pairs successfully amplified target loci and 15 SSRs showed high polymorphism.The alleles per locus ranged 6-50 on average of 25.3.The expected and observed heterozygosity varied from 0.632 to 0.969 and from 0.519 to 0.953,respectively.The polymorphic index content(PIC)values of each locus ranged 0.587-0.966 on average of 0.851.Among six yellowfin seabream population samples preliminarily tested for genetic diversity and differentiation,the Fangchenggang(FCG)population in Guangxi Province had the highest mean observed heterozygosity(H_(o))value(0.786),whereas the Zhangzhou(ZZ)population in Fujian Province had the lowest(0.678).The pairwise fixation index(Fst)values indicated significant population differentiation among six yellowfin seabream populations.This study provided evidence for the usefulness of the transcriptomic resource information and EST-SSR markers for natural resource conservation,population genetics,and breeding studies of yellowfin seabream in South China. 展开更多
关键词 yellowfin seabream Acanthopagrus latus full-length transcriptome expressed sequence tags linked to simple sequence repeats(EST-ssr)marker genetic diversity
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Analysis of Simple Sequence Repeats Information from Floral Expressed Sequence Tags Resources of Papaya (<i>Carica papaya</i>L.)
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作者 Priyanka Priyanka Dileep Kumar +2 位作者 Anurag Yadav Kusum Yadav U. N. Dwivedi 《American Journal of Plant Sciences》 2017年第9期2315-2331,共17页
Papaya (Carica papaya L.) is one of the most economically, medicinally and nutritionally important tropical fruit crops. Expressed sequence tags (ESTs) derived simple sequence repeat (SSR) markers are more valuable as... Papaya (Carica papaya L.) is one of the most economically, medicinally and nutritionally important tropical fruit crops. Expressed sequence tags (ESTs) derived simple sequence repeat (SSR) markers are more valuable as they are derived from conserved genic portion. Development of EST-SSRs markers through in silico approach is cheaper, less time consuming and labour-intensive. In this study, we aimed to mine SSRs and developed EST-SSR primers from papaya floral ESTs. A total of 75,846 papaya floral ESTs were downloaded from public database National Centre for Biotechnology Information (NCBI). A total of 26,039 floral unigenes (7961 contigs and 18,078 singletons) were generated after assembly of these ESTs. From these floral unigenes, 433,782 perfect SSRs, 204,968 compound SSRs and 6061 imperfect SSRs were mined, respectively. In perfect SSRs, mononucleotide repeats were most abundant (94.7%) followed by tri- (3.1%) and di-nucleotide repeats (1.7%). The frequencies of tetra-, hexa- and penta-nucleotide repeats accounted for only (0.17%), (0.04%) and (0.03%), respectively. In mononucleotide repeats, the most abundant motif was A/T (69.3%) and in di- and tri-nucleotide repeats were AG/CT (61%) and AAG/CTT (31%), respectively. In imperfect SSRs, mononucleotide repeats (56.5%) were most abundant. 176 different types of motifs were identified. A total of 3807 primer pairs for floral papaya ESTs were successfully designed. These developed EST-SSR primers are being used for the genetic improvement of papaya such as study of cross-transferability across genera/species, evaluation of genetic diversity, and identification of sex-specific markers. These EST derived SSRs can also be used in filling gaps in existing linkage maps in papaya. 展开更多
关键词 PAPAYA (Carica PAPAYA L.) In Silico simple sequence repeats Expressed sequence Tags (ESTs) ssr Mining EST-ssr ssr Motifs Primer Pairs
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The genome of herpes simplex virus type 1 is prone to form short repeat sequences
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作者 Xiangyan Zhao Xiaolong Wu +4 位作者 Lv Qin Zhongyang Tan Shifang Li Qingjian Ouyang You Tian 《Journal of Biosciences and Medicines》 2013年第3期26-30,共5页
Herein, we report a very high content of simple sequence repeats (SSRs) covering 66.12% of the herpes simplex virus type 1 (HSV-1) genome when a low threshold is adopted to define SSRs, indicating that repeat sequence... Herein, we report a very high content of simple sequence repeats (SSRs) covering 66.12% of the herpes simplex virus type 1 (HSV-1) genome when a low threshold is adopted to define SSRs, indicating that repeat sequence is a very important character of the HSV-1 genome. The repeats with two iterations account for 68.33% of the total repeats. In reality, the genome of HSV-1 is prone to form shorter repeat sequences. For mono-, di- and trinucleotide repeats, the repeat numbers decreased with the increase of repeats iterations, implicating that the formation tendency of SSRs might be from low iterations to high iterations. The high iterations SSRs might have subjected to strong selected pressure and survived to perform different functions. The analysis suggested that the repeats formation may be an essential evolutionary driving force for the HSV-1 genome, and the results might be helpful for studying the genome structure, repeats genesis and genome evolution of HSV-1. 展开更多
关键词 simple sequence repeat HSV-1 GENOME MICROSATELLITE ssr
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基于SSR标记与农艺性状对三七集团选择群体的评价
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作者 李满桥 王前 +6 位作者 李葵秀 俎峰 陈中坚 王勇 魏富刚 杨生超 刘冠泽 《植物遗传资源学报》 CAS CSCD 北大核心 2024年第10期1673-1684,共12页
三七为人参属多年生草本植物,生长和繁育周期长,群体间的遗传多样性低,但群体内单株间表型变异大,人参皂苷含量差异尤为明显。本研究根据三七中5种人参皂苷(三七皂苷R1、人参皂苷Rg1、人参皂苷Rb1、人参皂苷Re、人参皂苷Rd)含量构建了1... 三七为人参属多年生草本植物,生长和繁育周期长,群体间的遗传多样性低,但群体内单株间表型变异大,人参皂苷含量差异尤为明显。本研究根据三七中5种人参皂苷(三七皂苷R1、人参皂苷Rg1、人参皂苷Rb1、人参皂苷Re、人参皂苷Rd)含量构建了11份集团群体(SL1~SL11),对当代和第一代集团群体人参皂苷含量进行了比较分析。同时,基于三七基因组,使用MISA软件进行全基因组水平SSR标记开发,鉴定到255239个SSR标记,筛选出17对多态性SSR标记。使用SSR标记对第一代群体进行遗传多样性评价。结果表明,11份第一代集团群体观察杂合度Ho较高(0.4583~0.6042),遗传分化程度低(Fst=0.0447),且具有较高基因流(Nm=11.6189);第一代群体间总皂苷含量无显著性差异而三七皂苷R1变异系数高于总皂苷和其他单体皂苷,且群体SL8三七皂苷R1含量显著高于其他群体。综上,本研究以皂苷含量为目标性状构建了高皂苷含量的集团群体,并利用SSR标记评价了群体遗传多样性,构建的三七皂苷R1高含量群体可作为后续育种材料。 展开更多
关键词 三七 集团群体 ssr标记 人参皂苷
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基于EST-SSR标记的沙棘品种鉴定及指纹图谱构建
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作者 赵雨欣 张哲文 +5 位作者 考惠霞 孙永江 辛智鸣 赵喆 董树斌 程瑾 《生态与农村环境学报》 CAS CSCD 北大核心 2024年第3期374-385,共12页
以沙棘(Hippophae rhamnoides)优良品种“实优1号”为材料,对其叶片进行转录组测序,利用微卫星识别软件(microsatellite identification tool,MISA)和Primer 3(version 2.3.4)对获得的序列进行简单重复序列(simple sequence repeat,SSR... 以沙棘(Hippophae rhamnoides)优良品种“实优1号”为材料,对其叶片进行转录组测序,利用微卫星识别软件(microsatellite identification tool,MISA)和Primer 3(version 2.3.4)对获得的序列进行简单重复序列(simple sequence repeat,SSR)位点挖掘和引物设计,以收集的42份沙棘品种为研究材料,开展聚合酶链式反应(PCR)和毛细管电泳检测,旨在开发一套多态性高、稳定性好和通用性强的表达序列标签微卫星(express sequence tags from simple sequence repeat,EST-SSR)引物,构建沙棘指纹图谱,从而实现沙棘品种的快速准确鉴定,并对沙棘品种间亲缘关系进行分析。“实优1号”转录组测序共获得6196个SSR位点,其中,重复基元类型为182种,SSR基序长度主要分布在10~21 bp区间,占全部SSR的81.58%,主要SSR重复类型为单核苷酸重复(48.72%)、二核苷酸重复(22.68%)和三核苷酸重复(18.85%)。利用筛选出的28对引物在42份沙棘品种中共检测出193个等位基因,等位基因数(Na)、有效等位基因数(Ne)、观测杂合度(Ho)、期望杂合度(He)、多态信息含量(PIC)和Shannon信息指数(I)等遗传多样性参数的均值分别为6.964、3.495、0.617、0.671、0.623和1.384。UPGMA聚类分析表明,42份沙棘品种间的遗传相似性系数为0.601~0.990,当遗传相似性系数为0.694时,供试品种可分为2组;当遗传相似性系数约为0.7402时,供试品种可分为3组。优选6对引物构建指纹图谱,可以实现沙棘品种的快速准确鉴定。该研究可为沙棘的良种鉴定、指纹图谱构建以及遗传多样性和亲缘关系分析等提供分子水平的理论基础和数据支撑。 展开更多
关键词 沙棘 表达序列标签微卫星 指纹图谱 遗传多样性
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水芹SSR分子标记开发与遗传多样性分析
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作者 邢啸林 陈丹 +3 位作者 况勇 徐文娟 黄然 甘德芳 《江苏农业学报》 CSCD 北大核心 2024年第7期1285-1296,共12页
水芹是伞形科水芹属多年生草本植物,是一种重要的药食两用蔬菜作物。在中国,水芹的种植区域十分广泛,然而目前对其种质资源的鉴定、培育及遗传信息的研究较少。本研究利用溧阳白芹基因组开发水芹简单重复序列(SSR)分子标记,分析55份水... 水芹是伞形科水芹属多年生草本植物,是一种重要的药食两用蔬菜作物。在中国,水芹的种植区域十分广泛,然而目前对其种质资源的鉴定、培育及遗传信息的研究较少。本研究利用溧阳白芹基因组开发水芹简单重复序列(SSR)分子标记,分析55份水芹的遗传多样性并用非加权组平均法(UPGMA)构建系统进化树,同时用SSR扩增条带数据构建DNA指纹图谱。结果显示,共鉴定到325699个SSR位点,其中单核苷酸SSR重复单元、二核苷酸SSR重复单元、三核苷酸SSR重复单元、四核苷酸SSR重复单元、五核苷酸SSR重复单元、六核苷酸SSR重复单元的出现频率分别为33.94%、54.62%、9.31%、1.66%、0.17%、0.29%,其中二核苷酸SSR重复单元数最多,有177887个,且A/T(占比为29.98%)和AT/AT(占比为35.70%)是较丰富的重复类型。UPGMA分析结果表明,33对高多态性引物[多态信息含量(PIC)>0.25]可将55份水芹材料分为4组。利用筛选出的4对引物(Oj-084、Oj-110、Oj-112、Oj-156)可以将55份水芹材料完全区分开,并且可构建指纹图谱。研究结果可为水芹种质资源鉴定、保护及分子遗传育种提供有力依据。 展开更多
关键词 水芹 简单重复序列(ssr)分子标记 聚类分析 遗传多样性
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Analysis of SSR in Citrus Sequences from EMBL Database 被引量:2
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作者 MENGHai-jun CAOQing-qin +3 位作者 HUZhi-yong LIUGao-ping CHENGYun-jiang DENGXiu-xin 《Agricultural Sciences in China》 CAS CSCD 2005年第7期501-506,共6页
Abundance of simple sequence repeat (SSR) in Citrus sequences from EMBL database was investigated by usingcomputer program MISA (MIcroSAtellite), which aimed to provide useful information for the development of SSR ma... Abundance of simple sequence repeat (SSR) in Citrus sequences from EMBL database was investigated by usingcomputer program MISA (MIcroSAtellite), which aimed to provide useful information for the development of SSR markers.Among 32 896 sequences of Citrus, 4 987 SSRs were found in 4 167 sequences and the average distance between SSRs wasapproximately 3.5 kb. Mononucleotide repeats (50.6%) were the most abundant repeats. And di-, tri-, tetra-, penta- andhexa-nucleotide repeats were 22.8, 25.2, 1, 0.08, and 0.36%, respectively. The most abundant motif was A/T followed indescending order by AG/CT, AC/GT, AT/TA. AAT/ATT, AAG/CTT, AGC/CGT, ACG/CTG and C/G. They comprised about90% of all microsatellites. Ten primer pairs were designed, and three of them produced clear visible bands among Citrusand its related genera. 展开更多
关键词 CITRUS simple sequence repeats ABUNDANCE markerS
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SSR分子标记在玉米研究中的应用
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作者 王若丁 钟鹏 +8 位作者 王建丽 高海娟 孙蕊 李伟 徐艳霞 杨曌 李莎莎 王晓龙 刘丽 《饲料博览》 CAS 2024年第1期76-80,共5页
SSR简单重复序列也称微卫星DNA,是由特异性的引物进行PCR扩增分析的一种分子标记技术。简要介绍了SSR分子标记的原理,分析了SSR分子标记在玉米的种质资源、品种纯度鉴定、真伪鉴定、遗传多样性、种质性状等方面的应用。通过研究表明:能... SSR简单重复序列也称微卫星DNA,是由特异性的引物进行PCR扩增分析的一种分子标记技术。简要介绍了SSR分子标记的原理,分析了SSR分子标记在玉米的种质资源、品种纯度鉴定、真伪鉴定、遗传多样性、种质性状等方面的应用。通过研究表明:能够利用SSR分子标记技术对玉米的品种纯度鉴定、真伪性鉴定、遗传结构、亲缘关系、优劣群体的划分、种质性状等方面进行分析,同时也能为以后研究玉米的遗传连锁图谱构建、分子标记辅助育种、基因定位和种质资源等方面提供参考。 展开更多
关键词 ssr 分子标记 玉米 遗传多样性
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基于SSR标记的MCID法鉴定新疆地方梨品种及其遗传多样性分析
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作者 毕清芮 马新院 +3 位作者 薛玉冉 樊国全 王邵鹏 牛莹莹 《江苏农业学报》 CSCD 北大核心 2024年第10期1933-1941,共9页
为深入探究新疆地方梨品种的遗传关系,本研究采用简单重复序列(SSR)标记技术对28个新疆地方梨品种进行遗传多样性分析。同时,利用人工绘制品种鉴别示意图(MCID)法建立品种鉴定图(CID)。结果表明,新疆地方梨品种间遗传差异较小,遗传分化... 为深入探究新疆地方梨品种的遗传关系,本研究采用简单重复序列(SSR)标记技术对28个新疆地方梨品种进行遗传多样性分析。同时,利用人工绘制品种鉴别示意图(MCID)法建立品种鉴定图(CID)。结果表明,新疆地方梨品种间遗传差异较小,遗传分化为中等程度。通过构建新疆地方梨品种的聚类树状图,发现28个新疆地方梨具有较高的遗传多样性,遗传相似性系数为0.52~0.98。群体结构分析结果表明,最佳群体群组数值(K)=3时新疆地方梨品种被划分为3个组,各品种之间存在普遍的基因交流。采用MCID法构建新疆地方梨品种的CID图谱,并验证了该方法的有效性。本研究结果可为今后梨种质资源评价和利用提供理论依据。 展开更多
关键词 简单重复序列(ssr) 遗传多样性 品种鉴定
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基于表型性状及SSR标记的天麻种质资源遗传多样性分析
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作者 王彩云 张翔宇 +4 位作者 成忠均 武新玲 柳敏 周茂嫦 周雪 《中药材》 CAS 北大核心 2024年第2期281-289,共9页
目的:研究天麻的遗传多样性,分析杂交、自交天麻种质资源间的差异。方法:以26个天麻种质资源为材料,基于形态学标记对各种质的株高、蒴果数、花序长度、蒴果长度、蒴果宽度、块茎长度、块茎宽度、单重、有效成分含量等表型性状进行方差... 目的:研究天麻的遗传多样性,分析杂交、自交天麻种质资源间的差异。方法:以26个天麻种质资源为材料,基于形态学标记对各种质的株高、蒴果数、花序长度、蒴果长度、蒴果宽度、块茎长度、块茎宽度、单重、有效成分含量等表型性状进行方差分析、聚类分析及相关性分析;结合SSR分子标记进行遗传多样性研究,并构建SSR指纹图谱。结果:天麻表型性状中,各性状的变幅不同,变幅较大的为蒴果重、单重、块茎长、鲜品产量、干品产量、天麻素含量、对羟基苯甲醇含量;变幅较小的为蒴果宽、茎秆粗、肚脐眼直径、横纹环数、折干率。相关性分析结果显示,部分性状间相关性显著;表型性状聚类结果显示,在阈值为11.32时,将天麻资源分为2大类群。从合成的7对引物中筛选出3对SSR特异性引物,PCR扩增获得较清晰的SSR指纹图谱。UPGMA聚类可明显区分天麻自交系及杂交系,与表型聚类分析结果较为一致。结论:利用形态学标记及SSR分子标记相结合的方法可有效区分天麻杂交组合及自交组合。 展开更多
关键词 天麻 形态学 简单重复序列标记 种质资源 多样性
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Parent-offspring relationship recognition based on SSR and mtDNA confirmed resource supplement effect of Fenneropenaeus chinensis release
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作者 Song Sun Ding Lyu +2 位作者 Xianshi Jin Xiujuan Shan Weiji Wang 《Acta Oceanologica Sinica》 SCIE CAS CSCD 2024年第2期156-160,共5页
The resource of Fenneropenaeus chinensis has declined sharply due to excessive fishing intensity,ecological changes and diseases.In order to supplement the fishing yield and restore resources of F.chinensis,the releva... The resource of Fenneropenaeus chinensis has declined sharply due to excessive fishing intensity,ecological changes and diseases.In order to supplement the fishing yield and restore resources of F.chinensis,the relevant authorities have carried out the activities of stock enhancement and releasing.It can increase biomass and recover resources.However,compared with increasing biomass,there were still few reports on its effect on the recovery of resources.Resource recovery is a process related to whether the released individuals can form a reproductive population.Up to now,there has been a lack of evidence whether the released F.chinensis can complete the entire life history,and form reproduction population.In this study,gravid female shrimp after spawning migration were captured from coastal waters of Haiyang,Qingdao,and Yellow Sea.After identifying parentage relationships using simple sequence repeat(SSR)and mtDNA haplotype,it was finally confirmed that there were eight released individuals in the recapture samples.It was confirmed for the first time that at least part of the released F.chinensis can complete overwintering and reproductive migration,and maintain the migration habits as their wild counterparts.Therefore,we infered that the released shrimp can reproduce under natural conditions,these F.chinensis can form reproductive populations theoretically if without human intervention.These results indicated that enhancenment and release activities have a positive effect on resource recovery. 展开更多
关键词 Fenneropenaeus chinensis RELEASE simple sequence repeat(ssr) mtDNA resource supplement
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Large scale identification of SSR marker in perilla by next generation sequencing 被引量:1
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作者 Qi Shen He Wen +5 位作者 Tianyuan Zhang Jing Xu Xianping Wang Shimei Yang Caifu Du Degang Zhao 《Oil Crop Science》 2019年第2期100-109,共10页
Perilla frutescens (L.) is an edible, medicinal crop, and most popular in East Asia. Its molecular breeding and research are hampered by the paucity of molecular markers. Simple sequence repeat (SSR) markers are ubiqu... Perilla frutescens (L.) is an edible, medicinal crop, and most popular in East Asia. Its molecular breeding and research are hampered by the paucity of molecular markers. Simple sequence repeat (SSR) markers are ubiquitous and widely used in eukaryotic genomes. EST-SSRs identification of perilla was performed in 116,387 reads generated by Illumina paired-end sequencing technology. In total 25,449 unigenes containing SSR and 33,867 SSR loci were identified, and 19,400 primer pairs were designed. Polymorphism of SSR primers was conducted by searching for insertions and deletions (INDELs), and 1,567 unique SSRs were predicted. Totally, 200 SSR primer pairs were selected for polymorphic validation among 23 perilla accessions. Results showed that 175 primer pairs produced amplicons, and 30 pairs exhibited polymorphism. Polymorphic ratio was higher by using INDEL method than using conventional primers. Phylogenetic analysis showed the 2 distinct groups: P. frutescens var. frutescens and P. frutescens var. crispa. Wrinkled leaf trait and seed trait were distinct between these 2 groups. However, no clear leaf color or geographic relationship was detected. The large scale development and identification of SSR marker in this research laid a foundation for genetic analysis and marker assisted breeding of cultivated perilla. 展开更多
关键词 PERILLA frutescens L. simple sequence repeatS (ssr) next generation sequencING INDEL marker-assisted BREEDING
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基于果形对草莓品种遗传多样性SSR分析
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作者 魏姗姗 赵强 +1 位作者 杨旭伟 武海福 《耕作与栽培》 2024年第1期33-38,47,共7页
本研究利用SSR分子标记技术对国家果树种质北京草莓圃的173份草莓品种进行区分,根据果形利用PopGene软件对其做了聚类分析。结果显示,长圆锥形、短圆锥形、阔圆锥形、圆锥形/长楔形、圆锥形/平楔形、长楔形、近圆形、圆球形/卵圆形的观... 本研究利用SSR分子标记技术对国家果树种质北京草莓圃的173份草莓品种进行区分,根据果形利用PopGene软件对其做了聚类分析。结果显示,长圆锥形、短圆锥形、阔圆锥形、圆锥形/长楔形、圆锥形/平楔形、长楔形、近圆形、圆球形/卵圆形的观测纯合度都为0.846 2,扁球形、圆球形/半圆球形、短圆锥形/短楔形的观测纯合度都在0.923 1~0.948 7之间,但是短圆形纯合度最低,为0.692 3,由此发现与其他形状的亲缘关系较远,其余形状相互之间的亲缘关系较近。根据果形分析SSR扩增等位基因的多态性发现,173份草莓品种整体纯合体偏多,其中楔形/长圆锥形的无杂合体,而短圆形的纯合体最少,草莓品种整体亲缘关系较近。 展开更多
关键词 草莓 ssr 遗传多样性 果形
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Assessment of genetic diversity by simple sequence repeat markers among forty elite varieties in the germplasm for malting barley breeding 被引量:5
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作者 Jun-mei WANG Jian-ming YANG Jing-huan ZHU Qiao-jun JIA Yue-zhi TAO 《Journal of Zhejiang University-Science B(Biomedicine & Biotechnology)》 SCIE CAS CSCD 2010年第10期792-800,共9页
The genetic diversity and relationship among 40 elite barley varieties were analyzed based on simple sequence repeat (SSR) genotyping data. The amplified fragments from SSR primers were highly polymorphic in the bad... The genetic diversity and relationship among 40 elite barley varieties were analyzed based on simple sequence repeat (SSR) genotyping data. The amplified fragments from SSR primers were highly polymorphic in the badey accessions investigated. A total of 85 alleles were detected at 35 SSR loci, and allelic variations existed at 29 SSR loci. The allele number per locus ranged from 1 to 5 with an average of 2.4 alleles per locus detected from the 40 badey accessions. A cluster analysis based on the genetic similarity coefficients was conducted and the 40 varieties were classified into two groups. Seven malting barley varieties from China fell into the same subgroup. It was found that the genetic diversity within the Chinese malting barley varieties was narrower than that in other barley germplasm sources, suggesting the importance and feasibility of introducing elite genotypes from different origins for malting barley breeding in China. 展开更多
关键词 Barley (Hordeum vu/gare L.) Genetic similarity simple sequence repeat (ssr marker Cluster analysis Genetic diversity
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