SSR Marker-Assisted Management of Parental Germplasm in Sugarcane (<i>Saccharum</i> spp. hybrids) Breeding Programs
Sugarcane (<i>Saccharum</i> spp. hybrids) is an important sugar and bioenergy crop with a high aneuploidy, complex genomes and extreme heterozygosity. A good understanding of genetic diversity and population structure among sugarcane parental lines is a prerequisite for sugarcane improve...
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| Format: | Article |
| Language: | English |
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MDPI AG
2019-08-01
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| Series: | Agronomy |
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| Online Access: | https://www.mdpi.com/2073-4395/9/8/449 |
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| author | Jiantao Wu Qinnan Wang Jing Xie Yong-Bao Pan Feng Zhou Yuqiang Guo Hailong Chang Huanying Xu Wei Zhang Chuiming Zhang Yongsheng Qiu |
| author_facet | Jiantao Wu Qinnan Wang Jing Xie Yong-Bao Pan Feng Zhou Yuqiang Guo Hailong Chang Huanying Xu Wei Zhang Chuiming Zhang Yongsheng Qiu |
| author_sort | Jiantao Wu |
| collection | DOAJ |
| description | Sugarcane (<i>Saccharum</i> spp. hybrids) is an important sugar and bioenergy crop with a high aneuploidy, complex genomes and extreme heterozygosity. A good understanding of genetic diversity and population structure among sugarcane parental lines is a prerequisite for sugarcane improvement through breeding. In order to understand genetic characteristics of parental lines used in sugarcane breeding programs in China, 150 of the most popular accessions were analyzed with 21 fluorescence-labeled simple sequence repeats (SSR) markers and high-performance capillary electrophoresis (HPCE). A total of 226 SSR alleles of high-resolution capacity were identified. Among the series obtained from different origins, the YC-series, which contained eight unique alleles, had the highest genetic diversity. Based on the population structure analysis, the principal coordinate analysis (PCoA) and phylogenetic analysis, the 150 accessions were clustered into two distinct sub-populations (Pop1 and Pop2). Pop1 contained the majority of clones introduced to China (including 28/29 CP-series accessions) while accessions native to China clustered in Pop2. The analysis of molecular variance (AMOVA), fixation index (<i>Fst</i>) value and gene flow (<i>Nm</i>) value all indicated the very low genetic differentiation between the two groups. This study illustrated that fluorescence-labeled SSR markers combined with high-performance capillary electrophoresis (HPCE) could be a very useful tool for genotyping of the polyploidy sugarcane. The results provided valuable information for sugarcane breeders to better manage the parental germplasm, choose the best parents to cross, and produce the best progeny to evaluate and select for new cultivar(s). |
| first_indexed | 2024-12-18T00:40:49Z |
| format | Article |
| id | doaj.art-7af67a309abe4c3ba2eb5a8db35b9567 |
| institution | Directory Open Access Journal |
| issn | 2073-4395 |
| language | English |
| last_indexed | 2024-12-18T00:40:49Z |
| publishDate | 2019-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Agronomy |
| spelling | doaj.art-7af67a309abe4c3ba2eb5a8db35b95672022-12-21T21:26:52ZengMDPI AGAgronomy2073-43952019-08-019844910.3390/agronomy9080449agronomy9080449SSR Marker-Assisted Management of Parental Germplasm in Sugarcane (<i>Saccharum</i> spp. hybrids) Breeding ProgramsJiantao Wu0Qinnan Wang1Jing Xie2Yong-Bao Pan3Feng Zhou4Yuqiang Guo5Hailong Chang6Huanying Xu7Wei Zhang8Chuiming Zhang9Yongsheng Qiu10Guangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangzhou 510316, ChinaGuangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangzhou 510316, ChinaGuangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangzhou 510316, ChinaSugarcane Research Unit, USDA-ARS, Houma, LA 70360, USAGuangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangzhou 510316, ChinaGuangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangzhou 510316, ChinaGuangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangzhou 510316, ChinaGuangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangzhou 510316, ChinaGuangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangzhou 510316, ChinaGuangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangzhou 510316, ChinaGuangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangzhou 510316, ChinaSugarcane (<i>Saccharum</i> spp. hybrids) is an important sugar and bioenergy crop with a high aneuploidy, complex genomes and extreme heterozygosity. A good understanding of genetic diversity and population structure among sugarcane parental lines is a prerequisite for sugarcane improvement through breeding. In order to understand genetic characteristics of parental lines used in sugarcane breeding programs in China, 150 of the most popular accessions were analyzed with 21 fluorescence-labeled simple sequence repeats (SSR) markers and high-performance capillary electrophoresis (HPCE). A total of 226 SSR alleles of high-resolution capacity were identified. Among the series obtained from different origins, the YC-series, which contained eight unique alleles, had the highest genetic diversity. Based on the population structure analysis, the principal coordinate analysis (PCoA) and phylogenetic analysis, the 150 accessions were clustered into two distinct sub-populations (Pop1 and Pop2). Pop1 contained the majority of clones introduced to China (including 28/29 CP-series accessions) while accessions native to China clustered in Pop2. The analysis of molecular variance (AMOVA), fixation index (<i>Fst</i>) value and gene flow (<i>Nm</i>) value all indicated the very low genetic differentiation between the two groups. This study illustrated that fluorescence-labeled SSR markers combined with high-performance capillary electrophoresis (HPCE) could be a very useful tool for genotyping of the polyploidy sugarcane. The results provided valuable information for sugarcane breeders to better manage the parental germplasm, choose the best parents to cross, and produce the best progeny to evaluate and select for new cultivar(s).https://www.mdpi.com/2073-4395/9/8/449sugarcaneparental linepopulation structureplant breedinggenetic diversitysimple sequence repeats (SSR) |
| spellingShingle | Jiantao Wu Qinnan Wang Jing Xie Yong-Bao Pan Feng Zhou Yuqiang Guo Hailong Chang Huanying Xu Wei Zhang Chuiming Zhang Yongsheng Qiu SSR Marker-Assisted Management of Parental Germplasm in Sugarcane (<i>Saccharum</i> spp. hybrids) Breeding Programs Agronomy sugarcane parental line population structure plant breeding genetic diversity simple sequence repeats (SSR) |
| title | SSR Marker-Assisted Management of Parental Germplasm in Sugarcane (<i>Saccharum</i> spp. hybrids) Breeding Programs |
| title_full | SSR Marker-Assisted Management of Parental Germplasm in Sugarcane (<i>Saccharum</i> spp. hybrids) Breeding Programs |
| title_fullStr | SSR Marker-Assisted Management of Parental Germplasm in Sugarcane (<i>Saccharum</i> spp. hybrids) Breeding Programs |
| title_full_unstemmed | SSR Marker-Assisted Management of Parental Germplasm in Sugarcane (<i>Saccharum</i> spp. hybrids) Breeding Programs |
| title_short | SSR Marker-Assisted Management of Parental Germplasm in Sugarcane (<i>Saccharum</i> spp. hybrids) Breeding Programs |
| title_sort | ssr marker assisted management of parental germplasm in sugarcane i saccharum i spp hybrids breeding programs |
| topic | sugarcane parental line population structure plant breeding genetic diversity simple sequence repeats (SSR) |
| url | https://www.mdpi.com/2073-4395/9/8/449 |
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