Genetic Analysis of Diversity within a Chinese Local Sugarcane Germplasm Based on Start Codon Targeted Polymorphism
Identifieur interne : 000A71 ( Main/Exploration ); précédent : 000A70; suivant : 000A72Genetic Analysis of Diversity within a Chinese Local Sugarcane Germplasm Based on Start Codon Targeted Polymorphism
Auteurs : Youxiong Que [République populaire de Chine] ; Yongbao Pan [États-Unis] ; Yunhai Lu [République populaire de Chine] ; Cui Yang [République populaire de Chine] ; Yuting Yang [République populaire de Chine] ; Ning Huang [République populaire de Chine] ; Liping Xu [République populaire de Chine]Source :
- BioMed Research International [ 2314-6133 ] ; 2014.
Abstract
In-depth information on sugarcane germplasm is the basis for its conservation and utilization. Data on sugarcane molecular markers are limited for the Chinese sugarcane germplasm collections. In the present study, 20 start codon targeted (SCoT) marker primers were designed to assess the genetic diversity among 107 sugarcane accessions within a local sugarcane germplasm collection. These primers amplified 176 DNA fragments, of which 163 were polymorphic (92.85%). Polymorphic information content (PIC) values ranged from 0.783 to 0.907 with a mean of 0.861. Unweighted pair group method of arithmetic averages (UPGMA) cluster analysis of the SCoT marker data divided the 107 sugarcane accessions into six clusters at 0.674 genetic similarity coefficient level. Relatively abundant genetic diversity was observed among ROC22, ROC16, and ROC10, which occupied about 80% of the total sugarcane acreage in China, indicating their potential breeding value on Mainland China. Principal component analysis (PCA) partitioned the 107 sugarcane accessions into two major groups, the Domestic Group and the Foreign Introduction Group. Each group was further divided based on institutions, where the sugarcane accessions were originally developed. The knowledge of genetic diversity among the local sugarcane germplasm provided foundation data for managing sugarcane germplasm, including construction of a core collection and regional variety distribution and subrogation.
Url:
DOI: 10.1155/2014/468375
PubMed: 24779012
PubMed Central: 3980922
Affiliations:
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first="Youxiong" last="Que">Youxiong Que</name><affiliation wicri:level="1"><nlm:aff id="I1">Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture/Fujian Agriculture and Forestry University, Fuzhou 350002, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture/Fujian Agriculture and Forestry University, Fuzhou 350002</wicri:regionArea><placeName><settlement type="city">Fuzhou</settlement><region type="province">Fujian</region></placeName></affiliation></author><author><name sortKey="Pan, Yongbao" sort="Pan, Yongbao" uniqKey="Pan Y" first="Yongbao" last="Pan">Yongbao Pan</name><affiliation wicri:level="1"><nlm:aff id="I2">USDA-ARS, Sugarcane Research Laboratory, Houma, LA 70360, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>USDA-ARS, Sugarcane Research Laboratory, Houma, LA 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Agriculture/Fujian Agriculture and Forestry University, Fuzhou 350002, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture/Fujian Agriculture and Forestry University, Fuzhou 350002</wicri:regionArea><placeName><settlement type="city">Fuzhou</settlement><region type="province">Fujian</region></placeName></affiliation></author><author><name sortKey="Yang, Yuting" sort="Yang, Yuting" uniqKey="Yang Y" first="Yuting" last="Yang">Yuting Yang</name><affiliation wicri:level="1"><nlm:aff id="I1">Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture/Fujian Agriculture and Forestry University, Fuzhou 350002, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture/Fujian Agriculture and Forestry University, Fuzhou 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Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture/Fujian Agriculture and Forestry University, Fuzhou 350002, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture/Fujian Agriculture and Forestry University, Fuzhou 350002</wicri:regionArea><placeName><settlement type="city">Fuzhou</settlement><region type="province">Fujian</region></placeName></affiliation></author></analytic><series><title level="j">BioMed Research International</title><idno type="ISSN">2314-6133</idno><idno type="eISSN">2314-6141</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>In-depth information on sugarcane germplasm is the basis for its conservation and utilization. Data on sugarcane molecular markers are limited for the Chinese sugarcane germplasm collections. In the present study, 20 start codon targeted (SCoT) marker primers were designed to assess the genetic diversity among 107 sugarcane accessions within a local sugarcane germplasm collection. These primers amplified 176 DNA fragments, of which 163 were polymorphic (92.85%). Polymorphic information content (PIC) values ranged from 0.783 to 0.907 with a mean of 0.861. Unweighted pair group method of arithmetic averages (UPGMA) cluster analysis of the SCoT marker data divided the 107 sugarcane accessions into six clusters at 0.674 genetic similarity coefficient level. Relatively abundant genetic diversity was observed among ROC22, ROC16, and ROC10, which occupied about 80% of the total sugarcane acreage in China, indicating their potential breeding value on Mainland China. Principal component analysis (PCA) partitioned the 107 sugarcane accessions into two major groups, the Domestic Group and the Foreign Introduction Group. Each group was further divided based on institutions, where the sugarcane accessions were originally developed. The knowledge of genetic diversity among the local sugarcane germplasm provided foundation data for managing sugarcane germplasm, including construction of a core collection and regional variety distribution and subrogation.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Chen, Rk" uniqKey="Chen R">RK Chen</name></author><author><name sortKey="Xu, Lp" uniqKey="Xu L">LP Xu</name></author><author><name sortKey="Lin, Yq" uniqKey="Lin Y">YQ Lin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Luo, J" uniqKey="Luo J">J Luo</name></author><author><name sortKey="Deng, Zh" uniqKey="Deng Z">ZH Deng</name></author><author><name sortKey="Que, Yx" uniqKey="Que Y">YX Que</name></author><author><name sortKey="Yuan, Zn" uniqKey="Yuan Z">ZN Yuan</name></author><author><name sortKey="Chen, Rk" uniqKey="Chen R">RK Chen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Baver, Ld" 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Chine</li><li>États-Unis</li></country><region><li>Fujian</li></region><settlement><li>Fuzhou</li></settlement></list><tree><country name="République populaire de Chine"><region name="Fujian"><name sortKey="Que, Youxiong" sort="Que, Youxiong" uniqKey="Que Y" first="Youxiong" last="Que">Youxiong Que</name></region><name sortKey="Huang, Ning" sort="Huang, Ning" uniqKey="Huang N" first="Ning" last="Huang">Ning Huang</name><name sortKey="Lu, Yunhai" sort="Lu, Yunhai" uniqKey="Lu Y" first="Yunhai" last="Lu">Yunhai Lu</name><name sortKey="Xu, Liping" sort="Xu, Liping" uniqKey="Xu L" first="Liping" last="Xu">Liping Xu</name><name sortKey="Yang, Cui" sort="Yang, Cui" uniqKey="Yang C" first="Cui" last="Yang">Cui Yang</name><name sortKey="Yang, Yuting" sort="Yang, Yuting" uniqKey="Yang Y" first="Yuting" last="Yang">Yuting Yang</name></country><country name="États-Unis"><noRegion><name sortKey="Pan, Yongbao" sort="Pan, Yongbao" uniqKey="Pan Y" first="Yongbao" last="Pan">Yongbao 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