Independently segregating simple sequence repeats (SSR) alleles in polyploid sugarcane

Authors: Pan, Yong-Bao; LIU, PINGWU - Collaborator; QUE, YOUXIONG - Fujian Agricultural & Forestry University

Submitted to: Sugar Tech
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/2/2014
Publication Date: 8/7/2014
Publication URL: http://handle.nal.usda.gov/10113/59714
Citation: Pan, Y.-B., Liu, P., Que, Y. 2014. Independently segregating simple sequence repeats (SSR) alleles in polyploid sugarcane. Sugar Tech. 17(3):235-242. DOI: 10.1007/s12355-014-0330-5.

Interpretive Summary: Sugarcane cultivars have a complex genetic makeup with 100-130 chromosomes that contain numerous genes (DNA segments or markers). How the DNA markers segregate during reproductive cell division and offspring production is a difficult genetics research subject. With the late development of two laboratory techniques, i.e., a capillary electrophoresis- and fluorescence-based DNA fingerprinting technique and a single pollen collection and PCR technique, we fingerprinted two sugarcane cultivars L 99-233 (male) and HoCP 00-950 (female), 92 individual pollens of L 99-233, and 162 offspring of the two cultivars with a SSR (simple sequence repeats) DNA marker SMC336BS. Five DNA fingerprints were found in L 99-233 and two in HoCP 00-950. Of these fingerprints, one was found in both cultivars. The presence or absence of these six parental fingerprints among both pollen and offspring was analyzed. The results demonstrated that segregation of molecular genetic markers is complicated in sugarcane. Only two of the four fingerprints segregated in an expected 50% presence to 50% absence ratio among both pollen and offspring populations. One allele segregated at 50%:50% among pollens, but unexpectedly at 75%:25% among the offspring. The allele found in both cultivars segregated at 50%:50% among pollens, but was found in almost every offspring, probably due to its homozygosis in female cultivar. The genetic knowledge from this study will provide some guidance for marker-assisted selection and may lead to additional studies involving pollen and offspring of reciprocal crosses involving both cultivars.

Technical Abstract: The complex nuclear genomic and flower structures of sugarcane cultivars (Saccharum hybrids spp., 2n = 10x = 100 – 130) render sugarcane a difficult subject for genetics research. Using a capillary electrophoresis- and fluorescence-labeling-based SSR genotyping platform, the segregation of a multi-allelic sugarcane SSR marker SMC336BS was investigated among single pollens of a sugarcane cultivar L 99-233 as well as its F1 progenies of a bi-parental cross between HoCP 00-950 (female) and L 99-233 (male). L 99-233 produced five reproducible SSR alleles, namely, 6-154, 6-167, 6-169, 6-171, and 6-175, while HoCP 00-950 produced two SSR alleles, 6-166 and 6-169. Of these six parental alleles, 6-167, 6-169, 6-171, and 6-175 were detected in approximately half of the pollens indicating an independent Mendelian segregation. In addition, four alleles, namely, 6-154, 6-166, 6-167, and 6-175, were detected in approximately half of the F1 progenies, again an indication of independent Mendelian segregation. Twenty-two pollen genotypes were observed among 92 single pollens at frequencies varying from 1.08% to 11.83% and 33 genotypes were observed among 162 F1 progenies at frequencies varying from 0.62% to 8.64%. Although none of the 92 single pollens amplified all five parental alleles, one F1 progeny produced all the six parental alleles. Unexpected segregation patterns were also observed. Allele 6-171, which was absent in HoCP 00-950, segregated at 3 presence:1 absence instead of expected 1:1. Allele 6-169, which was detected in both cultivars and segregated at 1:1 among pollens, segregated at nearly1:0. These unexpected segregation patterns may be associated with the complexity of sugarcane genome and illustrate the needs of additional genetic studies in polyploid sugarcane.