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Journal of Ocean University of China 2022年第5期21卷 1265-1272页

作者： NAN Ze XU Ran HOU Chunqiang ZHENG Xiaodong Institute of Evolution and Marine Biodiversity Ocean University of ChinaQingdao 266003China Key Laboratory of Mariculture Ocean University of ChinaQingdao 266003China Tianjin Fisheries Research Institute Tianjin 300457China

Octopus minor(Sasaki 1920)is an important commercial cephalopod species in *** species has declined sharply in recent ***,genetic studies of *** are imperative to exploit and manage the wild *** this study,46192 microsatellite loci were discovered in 70174 unigenes from the transcriptomic *** all of the simple sequence repeat(SSR)unit categories,di-nucleotide and tri-nucleotide SSRs accounted for 45.26%and 14.49%,respectively.A total of 108 SSRs were tested,of which 21 were neutral and *** SSRs were selected for genetics analyses of the *** populations in the Bohai Sea,the Yellow Sea,and the southwest coast of the Taiwan Strait *** pairwise F_(st) values were detected among the *** UPGMA tree based on genetic distances suggested that the sampling locations could be arranged in three *** markers are evidence that the populations in this region may be structured,with samples from Penghu differing remarkably from those in northern *** present study characterized genetic markers for population assessment,management,and conservation of ***.

关键词： Octopus minor transcriptome simple sequence repeats genetic divergence

Development of simple sequence repeats (SSR) markers of ramie and comparison of SSR and inter-SSR marker systems

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Progress in Natural Science:Materials International 2005年第2期15卷 42-47页

作者： ZHOU Jianlin1*, JIE Yucheng2*, JIANG Yanbo2, ZHONG Yingli1, LIU Yunhai1 and ZHANG Jian1**(1. Department of Biochemistry and Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China 2. Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science, Changsha 410006, China) Dept. of Biochem. and Molecular Biol Coll. of Life Science Hunan Normal Univ. Changsha 410081 China Inst. of Bast Fiber Crops Chinese Acad. of Agric Science Changsha 410006 China

Ramie (Boehmeria nivea L.) is an important bast fiber crop. To study genetic background of this species, we isolated and characterized microsatellite markers of ramie. A genomic library containing inserts of rapid amplification of polymorphic DNA (RAPD) fragments was constructed, and screened by PCR amplification using anchored simple sequence repeats as primers. A total of 26 clones were identified as positives, and 13 microsatellite loci were found after sequencing. The polymorphism of these 13 microsatellite loci was examined and the utility of simple sequence repeats (SSR) and inter-SSR (ISSR) marker systems for genetic characterization compared using 19 selected ramie cultivars. Both approaches successfully discriminated the 19 cultivars which differed in the amount of polymorphism detected. The level of polymorphism detected by SSR was 95.0%, higher than that by ISSR (72.3%), but the average polymorphism information content (PIC) of ISSR (0.651) was higher than that of SSR (0.441). The higher PIC value of ISSR suggests that ISSR is more efficient for fingerprinting ramie cultivars than SSR markers. However, because the SSR loci are codominant, they are more suitable for determining the homozygosity levels of ramie, constructing linkage map, quantitative trait loci study of complex traits and marker-assisted selection.

关键词： ramie (Boehmeria nivea L.Gaud) simple sequence repeats inter-simple sequence repeats

Identification and Characterization of simple sequence repeats (SSR) Markers Associated with Downy Mildew Resistance Locus “<i>RPV1</i>” in Grapes

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Advances in Bioscience and Biotechnology 2021年第11期12卷 371-387页

作者： Neetu Goyal Akshay Nag Roshni R. Samarth Anuradha Upadhyay Kashmir Singh Department of Biotechnology Panjab University Chandigarh India National Research Centre for Grapes Pune India

The cultivation of grapes is severely impacted by the emergence of downy mildew (DM) disease which negatively affects quality and yield possibly resulting in heavy losses. Due to certain shortcomings in the usage of fungicides and the development of new cultivars by plant breeding, marker assisted selection (MAS) will be an efficient alternative method to introduce desired genes into the cultivated varieties in a short time period. The simple sequence repeats (SSR) markers seem to be the most popular genetic marker of choice for MAS. In the present study, we identified 14 new SSR markers in RPV1 locus that are associated with downy mildew resistance in grapes. The characterization of the identified markers was carried out on the basis of various parameters such as types of repeat motifs, number of repeats, different classes and structure of microsatellites. Additionally, SSR genotyping in 56 different grape accessions was done to determine the susceptibility or resistance of these accessions to DM.

关键词： Downy Mildew Resistance Locus simple sequence repeats Genotyping

Identification of stably expressed QTL for resistance to black shank disease in tobacco(Nicotiana tabacum L.) line Beinhart 1000-1

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The Crop Journal 2018年第3期6卷 282-290页

作者： Yusheng Zhang Xuan Guo Xingxing Yan Min Ren Caihong Jiang Yazeng Cheng Liuying Wen Dan Liu Yu Zhang Mingming Sun Quanfu Feng Aiguo Yang Lirui Cheng Key Laboratory of Tobacco Improvement and Biotechnology Tobacco Research InstituteChinese Academy of Agricultural Sciences College of Plant Science and Technology Qingdao Agricultural University

Cigar line Beinhart 1000-1 has effective durable resistance to black shank(BS) and is considered one of the most resistant sources in tobacco(Nicotiana tabacum L.). To investigate the inheritance and identification of stable quantitative trait loci(QTL) for BS response, F2,BC1 F2 individuals and BC1 F2:3 lines were produced from a cross between Beinhart 1000-1 and Xiaohuangjin 1025. Two major quantitative trait loci(M-QTL) named qBS7 and qBS17 were repeatedly detected under different conditions. QTL qBS7 was mapped to the region between PT30174 and PT60621 and explained 17.40%–25.60% of the phenotypic variance under different conditions. The other QTL qBS17 in interval PT61564–PT61538 of linkage group 17 was detected in a BC1 F2 population in the field and in BC1 F2:3 in both the field and at the seedling stage, explaining 6.90% to 11.60% of the phenotypic variance. The results improve our understanding of the inheritance of resistance to BS and provide information that can be used in marker-assisted breeding.

关键词： Phytophthora nicotianae Quantitative trait locus Plant disease resistance simple sequence repeats

Analysis of Genetic Diversity of Processing Apple Varieties

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Agricultural Sciences in China 2006年第10期5卷 745-750页

作者： SONG Ye ZHAI Heng YAO Yu-xin LI Ming DU Yuan-peng College of Horticultural Science and Engineering Shandong Agricultural University Taian 271018 P.R.China

Genetic diversity of 18 processing apple varieties and two fresh varieties were evaluated using 12 simple sequence repeats （SSR） primer pairs previously identified in Malus domestica Borkh. A total of 87 alleles in 10 loci were detected using 10 polymorphic SSR markers selected within the range of 5-14 alleles per locus. All the 20 varieties could be distinguished using two primer pairs and they were divided into four groups using cluster analysis. The genetic similarity （GS） of groups analyzed using cluster analysis varied from 0.14 to 0.83. High acid variety Avrolles separated from other varieties with GS less than 0.42. The second group contained Longfeng and Dolgo from Northeast of China, the inherited genes of Chinese crab apple. The five cider varieties with high tannin contents, namely, Dabinette, Frequin rouge, Kermerrien, ***, and *** were clustered into the third group. The fourth group was mainly composed of 12 juice and fresh varieties. Principal coordinate analysis （PCO） also divided all the varieties into four groups. Juice and fresh apple varieties, Longfeng and Dolgo were clustered together, respectively, using both the analyses. Both the analyses showed there was much difference between cider and juice varieties, cider and fresh varieties, as well as Chinese crab apple and western European crab apple, whereas juice varieties and fresh varieties had a similar genetic background. The genetic diversity and differentiation could be sufficiently reflected by combining the two analytical methods.

关键词： processing apple varieties genetic diversity simple sequence repeats cluster analysis principal coordinate analysis

Identification of quantitative trait loci for growth traits in red swamp crayfish(Procambarus clarkii)

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Aquaculture and Fisheries 2023年第6期8卷 727-736页

作者： Junxiao Sun Cuirong Luo Bo Peng Guohui Peng Yunfei Tan Xufeng Bai National Key Laboratory of Crop Genetic Improvement Shuangshui ShuanglüInstituteHuazhong Agricultural UniversityWuhan430070China Hubei Hongshan Laboratory Wuhan430070China College of Fisheries Huazhong Agricultural UniversityWuhan430070China College of Life Science and Technology Huazhong Agricultural UniversityWuhan430070China Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt Ministry of EducationWuhan430070China

Genetic breeding is an important approach to improve the economic traits of aquaculture ***,the genetic basis for important economic traits of red swamp crayfish,including growth-related traits,has not yet been *** the present study,two full-sib families and two natural populations were employed to identify quantitative trait loci(QTLs)for growth-related traits of red swamp *** total,28 QTLs for five growth-related traits,including body weight,body length,carapace length,carapace width,and abdomen length,were repeatedly identified in more than two families/populations,by means of association analysis;nine of these displayed a heterosis *** phenotypic variations of the five investigated traits explained by the 28 QTLs ranged from 4.2%to 19.0%.Eight additive and three heterosis QTLs were further successfully validated using comparative analysis of favoured alleles between the small and big size crayfish groups in the natural *** conclusion,this study investigated the genetic basis of growth-related traits in red swamp crayfish,which is of great significance for their application in the future molecular breeding of the species.

关键词： Red swamp crayfish(Procambarus clarkii) Growth-related traits simple sequence repeats Association analysis Quantitative trait loci

Comparative Analysis of Genetic Diversity and Structure in Rice Using ILP and SSR Markers

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Rice science 2010年第4期17卷 257-268页

作者： HUANG Ming XIE Fang-min CHEN Li-yun ZHAO Xiang-qian L. JOJEE D. MADONNA Rice Research Institute Hunan Agricultural University Changsha 410128 China Plant Breeding Genetics and Biotechnology Division International Rice Research Institute Metro Manila DAPO Box 7777 Philippines Grain Quality Nutrition and Postharvest Center International Rice Research Institute Metro Manila DAPO Box 7777 Philippines

Genetic diversity of 36 rice entries from the United States Department of Agriculture （USDA） rice collection was assessed using 103 ILP （intron length polymorphism） and 54 SSR （simple sequence repeats） markers. A total of 236 and 332 alleles were detected by the ILP and SSR markers, respectively. On average, the SSR markers produced higher polymorphism information content value and number of alleles than the ILP markers. Whereas the Nei＇s genetic distance measured using the SSR markers was much higher than that measured using the ILP markers. Manters test indicated that there was a statistically significant correlation （r=0.827, P〈0.001 ） between the two marker systems. UPGMA clustering based on the ILP and SSR markers resulted in consensus dendrograms. The cophenetic correlation coefficient （r=0.918, 0.878 and 0.924, P〈0.001 for the ILP, SSR and combined markers, respectively） showed a highly accurate dendrogram represented the genetic distance among these entries. The 36 entries were divided into four groups. Four African Oryza glaberrima accessions were clustered within a distinct group （I）, and the remaining entries were separated into three groups （11, III and IV）. All the entries could be also clustered into two main groups： One was composed of III and IV, considered as indica group, and the other was composed of I （O. glaberrima） and II （japonica-like）. Model-based cluster analysis revealed that the japonica-like group maintained very pure ancestry while the indica group shared mixed ancestry, especially for group III, which had seven admixtures sharing from 19.5% to 30.0% of ancestry with group IV （based on SSR markers）. It is suggested that ILP and SSR markers could be very useful for the genetic study and breeding in rice.

关键词： rice genetic diversity cluster analysis structure simple sequence repeats intron length polymorphism

Relationship Between Heterosis and Parental Genetic Distance Based on Molecular Markers for Functional Genes Related to Yield Traits in Rice

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Rice science 2010年第4期17卷 288-295页

作者： ZHANG Tao NI Xian-lin JIANG Kai-feng DENG Hua-feng HE Qing YANG Qian-hua YANG Li WAN Xian-Qi CAO Ying-jiang ZHENG Jia-kui Rice and Sorghum Research Institute Sichuan Academy of Agricultural Sciences Deyang 618000 China Luzhou Branch of Chinese National Center for Rice Improvement Luzhou 646000 China College of Bioengineering Chongqing UniversiO Chongqing 400044 China China National Hybrid Rice R ＆ D Center Changsha 410125 China

The genetic distances among 18 cytoplasmic male sterile lines and 11 restorer lines were analyzed with molecular markers derived from yield-related functional genes. The correlation between parental genetic distance and heterosis was investigated by analyzing the performance of 47 combinations. The results showed that the genetic distance was significantly correlated with yield heterosis （r=0.29^＊）, but not significantly correlated with heterosis for other traits, such as number of effective panicles per plant, seed setting rate, 1000-grain weight, number of grains per panicle and theoretical yield. However, the correlation coefficient was so small that the parental genetic distance could not to be used to predict heterosis.

关键词： rice yield related traits simple sequence repeats genetic distance heterosis correlation

Analysis of SSR in Citrus sequences from EMBL Database

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Agricultural Sciences in China 2005年第7期4卷 501-506页

作者： MENGHai-jun CAOQing-qin HUZhi-yong LIUGao-ping CHENGYun-jiang DENGXiu-xin NationalKeyLaboratoryofCropGeneticImprovement HuazhongAgriculturalUniversityWuhan430070P.R.China NationalKeyLaboratoryofCropGeneticImprovement HuazhongAgriculturalUniversityWuhan430070P.R.China／／DepartmentofBiotechnologyBeijingAgriculturalCollegeBeijing102206P.R.China

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 *** 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.

关键词： Citrus simple sequence repeats Abundance Markers

Genetic Diversity of Chinese Temperate and Exotic Tropical, Subtropical Quality Protein Maize Inbreds by SSR Markers

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Agricultural Sciences in China 2004年第2期3卷 94-100页

作者： FANXing-ming TANJing LIMing-shun YANGJun-yun CHENHong-mei InstituteofFoodCrops YunnanAcademyofAgriculturalSciencesKunming650205P.R.China InstituteofCropsBreedingandCultivation ChineseAcademyofAgriculturalSciencesBeijing100081P.R.China

Information on genetic relationship is of great value to maize (Zea mays L.) breeding. Theobjectives of this study were: 1) to classify 22 quality protein maize (QPM) inbreds intodifferent groups by using simple sequence repeats (SSR) markers, which included exotictropical, subtropical and domestic temperate QPM and normal maize inbreds; 2) to examine theconsistency of grouping results obtained from SSR, specific combining ability (SCA) analysis,and genetic backgrounds of these inbreds. A set of 39 polymorphic SSR primers was selected from70 primer pairs, which detected 136 alleles among the 22 lines. The mean polymorphisminformation content was 0.55. Based on analysis of genetic similarities, five groups wereidentified including Luda Red Cob, Sipingtou, Reid, Lancaster and a miscellaneous group withseveral tropical inbreds which could not be classified into the above four groups. The resultsgenerally agreed with previous results based on analysis of yield combining ability andpedigree data.

关键词： Maize inbred line simple sequence repeats Genetic similarity Genetic group