SSR-based molecular identification and population structure analysis for the Yunrui-series sugarcane (Saccharum spp. hybrids) genotypes

Authors: TIAN, CHUN-YAN - Yunnan Academy Of Agriculture Sciences; ZHU, JIAN-RONG - Yunnan Academy Of Agriculture Sciences; Pan, Yong-Bao; LU, XIN - Yunnan Academy Of Agriculture Sciences; DONG, LI-HUA - Yunnan Academy Of Agriculture Sciences; BURNER, DAVID - Retired ARS Employee; TAO, LIAN-AN - Yunnan Academy Of Agriculture Sciences; WU, CAI-WEN - Yunnan Academy Of Agriculture Sciences; JING, YAN-FEN - Yunnan Academy Of Agriculture Sciences

Submitted to: Sugar Tech
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/26/2021
Publication Date: 1/9/2022
Citation: Tian, C., Zhu, J., Pan, Y.-B., Lu, X., Dong, L., Burner, D.M., Tao, L., Wu, C., Jing, Y. 2022. SSR-based molecular identification and population structure analysis for the Yunrui-series sugarcane (Saccharum spp. hybrids) genotypes. Sugar Tech. 24(5):1391–1403. https://doi.org/10.1007/s12355-021-01099-8.
DOI: https://doi.org/10.1007/s12355-021-01099-8

Interpretive Summary: The success of sugarcane cross breeding depends on the understanding and exploitation of new germplasm. Sugarcane breeders often choose crossing parents based on their phenotypes. This research aimed to construct a molecular fingerprint map for 104 Yunrui-series sugarcane parental clones, analyze the genetic diversity and population structure of these genotypes, and use these information to assess the effectiveness of the crossing breeding program. DNA samples were prepared from the 104 parental clones and unique simple sequence repeat (SSR) DNA fragments were amplified via PCR using 21 pairs of fluorescence-labeled highly polymorphic PCR primers The SSR fragments along with DNA size standards were subjected to capillary electrophoresis (CE) platform. The resulting CE run files were processed by a DNA fingerprinting software GeneMarker and the presence or absence of a particular SSR fragment in each clone was scored. In total, 136 SSR fragments were detected. The presence or absence of these SSR fragments in each of the 103 clones was used to construct the molecular fingerprint map, calculate a few genetic diversity values, such as percentage of polymorphic loci (PPL), polymorphism information content (PIC), K, Q., and pairwise genetic differentiation (Fst), for genetic relationship and population structure analysis. The genetic analysis results divided the 104 parentaql clones into four populations and revealed a moderate to high level of genetic diversity, but a low level of genetic differentiation among these clones. This was due to the multiple events of crossing and backcrossing involving a limited number of parents. It is recommended that in addition to phenotypes, sugarcane breeders should also consider the genetic distance and population structure information when choosing parental clones.

Technical Abstract: The success of sugarcane cross breeding depends on the understanding and exploitation of new germplasm. Sugarcane breeders often choose crossing parents based on phenotypes. In this study, an SSR fingerprint map of 104 Yunrui-series sugarcane genotypes was constructed and the genetic diversity and population structure of these genotypes were analyzed using 21 pairs of fluorescence-labeled highly polymorphic SSR markers and a capillary electrophoresis platform. One hundred and thirty-six SSR fragments were detected. The average percentage of polymorphic loci (PPL) was 98.25%, and the mean of polymorphism information content (PIC) was 0.88. A neighbor-joining tree and population structure analysis divided the 104 genotypes into four pop-ulations with a Q value of < 0.6 for half of the genotypes. Pairwise genetic differentiation (Fst) between populations ranged from 0.009 to 0.023. Analysis of molecular variance (AMOVA) re-vealed that 98% of the variations occurred within the populations with a significant Fst value of 0.018 (p<0.001). The results revealed that Yunrui-series sugarcane genotypes share a moderate to high level of genetic diversity, but a low level of genetic differentiation due to multiple events of crossing and backcrossing involving a limited parental germplasm resource. Therefore, sugarcane breeders should take the genetic distance and population structure information, rather than phe-notypic performance alone, into consideration when choosing parental genotypes for cross breed-ing programs.