Segregation analysis of microsatellite (SSR) markers in sugarcane polyploids

Authors: LU, XIN - Yunnan Academy Of Agriculture Sciences; ZHOU, HUI - Yunnan Academy Of Agriculture Sciences; Pan, Yong-Bao; CHEN, CHARLES - Auburn University; ZHU, JIAN-RONG - Yunnan Academy Of Agriculture Sciences; CHEN, PING-HUA - Guangxi Academy Of Agricultural Sciences; CAI, QING - Yunnan Academy Of Agriculture Sciences; CHEN, RU-KAI - Fujian Agricultural & Forestry University

Submitted to: Genetics and Molecular Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/3/2015
Publication Date: 12/23/2015
Publication URL: http://handle.nal.usda.gov/10113/61893
Citation: Lu, X., Zhou, H., Pan, Y.-B., Chen, C.Y., Zhu, J., Chen, P., Cai, Q., Chen, R. 2015. Segregation analysis of microsatellite (SSR) markers in sugarcane polyploids. Genetics and Molecular Research. 14(4):18384-18395. DOI: 10.4238/2015.December.23.26.

Interpretive Summary: Cultivated sugarcane has a highly complicated genome involving at least 10 sets of at least 10 chromosomes per set. To understand how DNA markers segregate during reproductive cell and offspring production has been a tough research area. The late development of capillary electrophoresis-based sugarcane microsatellite (SSR) DNA fingerprinting and high throughput single pollen collection and PCR techniques have enabled genetic research in this area. In this study, a high throughput SSR DNA fingerprinting experiment was conducted involving 964 single pollen grains and 288 self-pollinated offspring from a Louisiana sugarcane cultivar LCP 85-384. Through PCR, five SSR DNA markers, namely, SMC336BS, SMC1604SA, SCM7, UGSM10, and UGSM97, primed the amplification of 20 distinctive, reproducible DNA fingerprints. The partition of each fingerprint among both pollen and offspring was analyzed. The results showed that each SSR fingerprint segregated in accordance with Mendelian genetics laws, that polymorphism information content value of the five SSR markers was greater on pollen than S1 offspring, and that fewer SSR genotypes were observed among S1 offspring than pollen population. Interestingly, Only 11 out of the 20 SSR fingerprints (55%) segregated in accordance with Mendelian segregation ratios expected from a 10x polyploid. The results will provide some guidance for sugarcane breeders in selecting crossing parents, estimating optimum size of seedling population, and enhancing efficient selection.

Technical Abstract: Although the microsatellite (SSR) DNA markers have been extensively used in sugarcane breeding research, little is known about its inheritance mechanism. To address this problem, a high throughput molecular genotyping experiment was conducted on 964 single pollen grains and a 288-self progeny S1 mapping population of a Louisiana sugarcane cultivar LCP 85-384. Through PCR, five polymorphic SSR markers (SMC336BS, SMC1604SA, SCM7, UGSM10, and UGSM97) primed the amplification of 20 alleles. Segregation analysis of each allele among both pollen and S1 populations showed the following: 1) Inheritance of each SSR allele was in accordance with the Mendelian laws of segregation and independent assortment; 2) The polymorphism information content (PIC) values of the five SSR markers based on the pollen population were greater than those based on the S1 population, probably due to the sharing of same alleles between female and male gametes; 3) Fewer SSR genotypes were observed for each SSR marker from the S1 population than those from the pollen population; and 4) Only 11 out of the 20 SSR alleles (55%) segregated in accordance with Mendelian segregation ratios expected from S1 and pollen populations of a 2n = 10 polyploid. The results from this study will provide some guidance for sugarcane breeders in selecting crossing parents, estimating optimum size of seedling population, and promoting efficient selection.