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ARS Home » Southeast Area » Houma, Louisiana » Sugarcane Research » Research » Publications at this Location » Publication #317184
Title: Genetic diversity analysis of sugarcane germplasm based on fluorescence-labeled simple sequence repeat markers and a capillary electrophoresis-based genotyping platform

Author
item YOU, QIAN - Fujian Agriculture And Forest University
item Pan, Yong-Bao
item XU, LI-PING - Fujian Agriculture And Forest University
item GAO, SHI-WU - Fujian Agriculture And Forest University
item WANG, QIN-NAN - Collaborator
item SU, YA-CHUN - Fujian Agriculture And Forest University
item YANG, YONG-QING - Fujian Agriculture And Forest University
item WU, QI-BIN - Fujian Agriculture And Forest University
item ZHOU, DING-GANG - Fujian Agriculture And Forest University
item QUE, YOU-XIONG - Fujian Agriculture And Forest University

Submitted to: Sugar Tech
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/28/2015
Publication Date: 6/29/2016
Publication URL: https://handle.nal.usda.gov/10113/63047
Citation: You, Q., Pan, Y.-B., Xu, L.-P., Gao, S.-W., Wang, Q.-N., Su, Y.-C., Yang, Y.-Q., Wu, Q.-B., Zhou, D.-G., Que, Y.-X. 2016. Genetic diversity analysis of sugarcane germplasm based on fluorescence-labeled simple sequence repeat markers and a capillary electrophoresis-based genotyping platform. Sugar Tech. 18:380-390. DOI: 10.1007/s12355-015-0395-9.

Interpretive Summary: Cross breeding is the most effective way for developing new sugarcane cultivars. Designing the best cross combinations is the foundation of a good cross breeding program that requires a complete knowledge of the genetic diversity among sugarcane germplasm and elite cultivars used as crossing parents. In this study, seven chromosome-derived microsatellite markers (gSSRs) and eight gene-derived microsatellite markers (EST-SSRs) were used to investigate the distribution of these markers among 181 sugarcane parental clones based on a fluorescence- and capillary electrophoresis-based detection system. Twenty-four of the 181 clones were developed in the U.S. that were introduced into the Chinese sugarcane breeding programs under several cooperative research agreements. One Mexican clone and one Brazilian clone were also included. The remaining clones were bred in China. A total of 205 different DNA fragments alleles were found; and analysis of their distribution among the 181 clones suggested that each type of DNA marker was able to uncover genetic diversity among the 181 clones at an equal level with average polymorphic information content value of 0.94 (gSSRs) and 0.93 (EST-SSRs), respectively. Two other genetic parameters, namely, gene differentiation coefficients (Gst) and gene flow values (Nm) were also determined. Neighbor-joining statistical analysis of the SSR distribution data sorted the 181 clones into seven groups. Four groups (IV, V, VI, and VII) contained CP-, HoCP-, or LCP-series clones from the USA. Three major groups, namely, the USA Group, the Guangxi-Hainan-Fujian Group, and the Guangdong Group, were comprised of 36, 64 and 39 clones, respectively. The new knowledge on genetic diversity through genotyping provides valuable information for selecting parents, designing cross combinations, and planning future cross breeding strategies.

Technical Abstract: Genetic diversity analysis, which refers to the elaboration of total extent of genetic characteristics in the genetic makeup of a certain species, constitutes a classical strategy for the study of diversity, population genetic structure, and breeding practices. In this study, fluorescence-labeled seven gSSR and eight EST-SSR primer pairs and a capillary electrophoresis genotyping platform were used to assess the genetic diversity among 181 sugarcane clones. The clones were sorted into 14 series based on their origin. A total of 205 polymorphic SSR alleles were identified. The mean polymorphic information content (PIC) value was 0.94 for gSSRs and 0.93 for EST-SSRs, respectively. Gene differentiation coefficient (Gst) of inter-series variation (13.71%) was much lower than intra-series variation (86.29%). Gene flow value (Nm=3.15) suggested that there was no significant genetic differentiation or population structure variations among the 14 series. The 181 clones could be clustered into seven groups based on Neighbor-joining cluster analysis. Three major groups, namely, the USA Group, the Guangxi-Hainan-Fujian Group, and the Guangdong Group, consisted of 36, 64 and 39 clones, respectively. This genotyping data provides valuable information for selecting cross parents, designing cross combinations, and future hybrid breeding strategies.