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ARS Home » Southeast Area » Houma, Louisiana » Sugarcane Research » Research » Publications at this Location » Publication #337151
Title: Molecular identification and genetic diversity analysis of Chinese sugarcane (Saccharum spp. hybrids) varieties using SSR markers

Author
item AHMAD, ALI - Fujian Agriculture And Forest University
item WANG, JIN-DA - Fujian Agriculture And Forest University
item Pan, Yong-Bao
item DENG, ZU-HU - Fujian Agriculture And Forest University
item CHEN, ZHI-WEI - Fujian Agriculture And Forest University
item CHEN, RU-KAI - Fujian Agriculture And Forest University
item GAO, SAN-JI - Fujian Agriculture And Forest University

Submitted to: Tropical Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/25/2017
Publication Date: 11/13/2017
Citation: Ahmad, A., Wang, J., Pan, Y., Deng, Z., Chen, Z., Chen, R., Gao, S. 2017. Molecular identification and genetic diversity analysis of Chinese sugarcane (Saccharum spp. hybrids) varieties using SSR markers. Tropical Plant Biology. Available: https://doi.org/10.1007/s12042-017-9195-6.

Interpretive Summary: Sugarcane (Saccharum spp. hybrids) is a major sugar and renewable bioenergy crop. Cultivated sugarcane plants are very unique in their genetic makeups by having 10-13 sets of 10 chromosomes in the nucleus and their vegetative propagation through buds. Multiple-year and multiple-location evaluations are required to identify a superior sugarcane variety due to strong environment x gene interactions. Maintaining a correct variety identity may become a topic of concern sometimes. Therefore, this study was set up to construct the molecular identities of 91 Chinese sugarcane varieties using simple sequence repeats (SSR) DNA markers and to assess the extent of genetic diversity among these varieties. Two laboratory systems of detecting DNA fingerprints, namely, capillary electrophoresis (CE) and polyacrylamide gel electrophoresis (PAGE), were employed to detect a total of 151 fingerprints that were amplified through PCR with 21 pairs of SSR primers. The CE system detected 150 fingerprints (99.3%) and the PAGE system detected 119 fingerprints (78.8%). The presence or absence of these 151 in each variety in a linear order represented the variety’s molecular identity. The ability of each pair of SSR primers to reveal genetic diversity was also calculated as its polymorphism information content (PIC) value, which varied from 0.71-0.98 (averaging 0.90) by CE or from 0.55-0.95 (averaging 0.84) by PAGE. Primer pair SMC336BS, SMC31CUQ, or SMC597CS each produced more than 10 fingerprints that were detected by either CE or PAGE. UPGMA (Unweighted pair group method with arithmetic mean)-based clustering method yielded pair-wise similarity coefficients of 58% to 95% and classified the 91 varieties into four groups. Moreover, genetic similarity estimates among the four variety groups varied from 0.32 to 0.88, with a mean of 0.49. The information on molecular identity and genetic diversity will be very helpful in certifying sugarcane varieties, detecting variety mis-labeling, and selecting genetically diverse parental lines for crossing.

Technical Abstract: Sugarcane (Saccharum spp. hybrids) is an important sugar and renewable bioenergy crop. However, its complex aneupolyploidy genome and vegetative mode of propagation often cause difficulty in selection and some variety identity issues in a breeding program. Therefore, the present study was set up to establish the molecular identity (ID) of 91 Chinese national or provincial released sugarcane varieties and evaluate the extent of genetic diversity among these varieties using simple sequence repeats (SSR) DNA markers and two fingerprint-detecting systems, capillary electrophoresis (CE) and polyacrylamide gel electrophoresis (PAGE). A total of 151 polymorphic alleles were detected and used in the molecular identity construction, of which 150 (99.3%) were detected by CE and 119 (78.8%) were detected by PAGE. Primer pair SMC336BS, SMC31CUQ, or SMC597CS amplified more than 10 alleles, which were detected either by CE or by PAGE. Polymorphism information content (PIC) values varied from 0.71- 0.98 with an average of 0.90 for CE, or from 0.55-0.95 with an average of 0.84 for PAGE. Unweighted pair group method with arithmetic mean (UPGMA) method classified the 91 varieties into four major groups with pair-wise similarity coefficients ranging from 58% to 95%. Moreover, genetic similarity estimates within and between the four groups varied from 0.32 to 0.88, with a mean of 0.49. Our results illustrated that the 21 SSR primer pairs in combination with CE or PAGE detection system are very useful for molecular identity construction and genetic diversity assessment. The information will be helpful in molecular identification of sugarcane varieties and parental selection in sugarcane breeding.