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Open AccessArticle

SSR Marker-Assisted Management of Parental Germplasm in Sugarcane (Saccharum spp. hybrids) Breeding Programs

1
Guangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangzhou 510316, China
2
Sugarcane Research Unit, USDA-ARS, Houma, LA 70360, USA
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Agronomy 2019, 9(8), 449; https://doi.org/10.3390/agronomy9080449
Received: 11 July 2019 / Revised: 8 August 2019 / Accepted: 10 August 2019 / Published: 14 August 2019
(This article belongs to the Special Issue Molecular Marker Technology for Crop Improvement)
Sugarcane (Saccharum 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 (Fst) value and gene flow (Nm) 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). View Full-Text
Keywords: sugarcane; parental line; population structure; plant breeding; genetic diversity; simple sequence repeats (SSR) sugarcane; parental line; population structure; plant breeding; genetic diversity; simple sequence repeats (SSR)
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    Doi: 10.5281/zenodo.3317477
    Link: https://zenodo.org/record/3317477#.XSaNWCwjzEZ
    Description: Table S1. Utilization data of the most widely used 150 parental clones from sugarcane hybrid breeding programs in China during the recent five years. Table S2. Tabulated K values of 150 most popular parental clones from sugarcane hybrid breeding programs in China at K=1 to 10. Table S3. Sub-population assignment of the 150 most popular parental clones from the sugarcane breeding programs in China based on the Q values.
MDPI and ACS Style

Wu, J.; Wang, Q.; Xie, J.; Pan, Y.-B.; Zhou, F.; Guo, Y.; Chang, H.; Xu, H.; Zhang, W.; Zhang, C.; Qiu, Y. SSR Marker-Assisted Management of Parental Germplasm in Sugarcane (Saccharum spp. hybrids) Breeding Programs. Agronomy 2019, 9, 449.

AMA Style

Wu J, Wang Q, Xie J, Pan Y-B, Zhou F, Guo Y, Chang H, Xu H, Zhang W, Zhang C, Qiu Y. SSR Marker-Assisted Management of Parental Germplasm in Sugarcane (Saccharum spp. hybrids) Breeding Programs. Agronomy. 2019; 9(8):449.

Chicago/Turabian Style

Wu, Jiantao; Wang, Qinnan; Xie, Jing; Pan, Yong-Bao; Zhou, Feng; Guo, Yuqiang; Chang, Hailong; Xu, Huanying; Zhang, Wei; Zhang, Chuiming; Qiu, Yongsheng. 2019. "SSR Marker-Assisted Management of Parental Germplasm in Sugarcane (Saccharum spp. hybrids) Breeding Programs" Agronomy 9, no. 8: 449.

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