SSR marker-assisted management of parental germplasm in sugarcane (Saccharum spp. hybrids) breeding programs

Authors: WU, JIANTAO - Collaborator; WANG, QINNAN - Collaborator; XIE, JING - Collaborator; Pan, Yong-Bao; ZHOU, FENG - Collaborator; GUO, YUQIANG - Collaborator; CHANG, HAILONG - Collaborator; XU, HUANYING - Collaborator; ZHANG, WEI - Collaborator; ZHANG, CHUIMING - Collaborator; QIU, YONGSHENG - Collaborator

Submitted to: Agronomy Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/10/2019
Publication Date: 8/14/2019
Citation: Wu, J., Wang, Q., Xie, J., Pan, Y.-B., Zhou, F., Guo, Y., Chang, H., Xu, H., Zhang, W., Zhang, C., Qiu, Y. 2019. SSR marker-assisted management of parental germplasm in sugarcane (Saccharum spp. hybrids) breeding programs. Agronomy Journal. 9(8):449. https://doi.org/10.3390/agronomy9080449.
DOI: https://doi.org/10.3390/agronomy9080449

Interpretive Summary: Sugarcane breeding usually takes more than 12 years of efforts due to its complex heterozygous genetic makeup and extreme genetics by environment interaction. At first, the breeders make crosses between different parental lines to produce new seedlings for field evaluation and selection. A good understanding of the genetic diversity and population structure among the parental lines is a pre-requisite for designing good crosses. In this study, microsatellite DNA markers were used to fingerprint 150 most popular parental lines to generate molecular data for genetic analysis. Genomic DNA samples were prepared from the leaf tissues and then subjected to DNA fingerprinting by PCR amplification with 21 pairs of fluorescence-labeled SSR primers. Amplified PCR fingerprints were separated through high-performance capillary electrophoreses (HPCE) and sizes were calibrated against DNA size standards. The experiment produced 226 SSR fingerprints of high-resolution quality that were variably distributed among the 150 most popular parental lines. Several computer software programs were also used to calculate genetic diversity indices and analyse population structure. Based on the results, the 150 parental lines were clustered into two distinct sub-populations, Pop1 and Pop2. Pop1 contained the majority of foreign introduction lines, including the CP varieties from the U.S., while most of the parental lines from Mainland China belonged to Pop2. Genetic differentiation between the two sub-populations was low. The Yacheng-series lines of Pop2 displayed a high level of genetic diversity and the CP-series clones were elite parents of several Chinese cultivars. The results will help sugarcane breeders manage the parental germplasm, choose the best parents to cross, and produce the best progeny to evaluate and select for new cultivar.

Technical Abstract: Sugarcane (Saccharum spp. hybrids) is an important sugar and bioenergy crop with a high aneuploidy, complex genomes and extremely heterozygosity. A good understanding of genetic diversity and population structure among sugarcane parental lines is a pre-requisite for sugarcane improvement through breeding. In order to understand genetic characteristics of parental lines used in sugarcane breeding programs in China, 150 of the most popular parental accessions were analyzed with 21 fluorescence-labeled SSR markers and high-performance capillary electrophoresis (HPCE). A total of 226 SSR alleles of high-resolution capacity were identified. Among series obtained different origins, the YC series, which contained eight private alleles, had the highest genetic diversity. Based on population structure analysis, principal coordinate analysis (PCoA) and phylogenetic analysis, the 150 accessions were clustered into two distinct sub-populations (Pop1 and Pop2). Pop1 contained the majority of introduction clones (including 28/29 CP series accessions) while mostly accessions from Mainland China belonged to Pop2. Five percent variance among and 95% variance within sub-populations indicated a low genetic differentiation between the two groups. The results will help sugarcane breeders manage the parental germplasm, choose the best parents to cross, and produce the best progeny to evaluate and select for new cultivar.