Population Structure and Genetic Diversity Analysis in Sugarcane (Saccharum spp. hybrids) and Six Related Saccharum Species

Abstract

Sugarcane (Saccharum spp. hybrids) is one of the most important commercial crops for sugar, ethanol, and other byproducts production; therefore, it is of great significance to carry out genetic research. Assessing the genetic population structure and diversity plays a vital role in managing genetic resources and gene mapping. In this study, we assessed the genetic diversity and population structure among 196 Saccharum accessions, including 34 S. officinarum, 69 S. spontaneum, 17 S. robustum, 25 S. barberi, 13 S. sinense, 2 S. edule, and 36 Saccharum spp. hybrids. A total of 624 polymorphic SSR alleles were amplified by PCR with 22 pairs of fluorescence-labeled highly polymorphic SSR primers and identified on a capillary electrophoresis (CE) detection system including 109 new alleles. Three approaches (model-based clustering, principal component analysis, and phylogenetic analysis) were conducted for population structure and genetic diversity analyses. The results showed that the 196 accessions could be grouped into either three (Q) or eight (q) sub-populations. Phylogenetic analysis indicated that most accessions from each species merged. The species S. barberi and S. sinense formed one group. The species S. robustum, S. barberi, S. spontaneum, S. edule, and sugarcane hybrids merged into the second group. The S. officinarum accessions formed the third group located between the other two groups. Two-way chi-square tests derived a total of 24 species-specific or species-associated SSR alleles, including four alleles each for S. officinarum, S. spontaneum, S. barberi, and S. sinense, five alleles for S. robustum. and three alleles for Saccharum spp. hybrids. These species-specific or species-associated SSR alleles will have a wide application value in sugarcane breeding and species identification. The overall results provide useful information for future genetic study of the Saccharum genus and efficient utilization of sugarcane germplasm resources in sugarcane breeding.

Assessing the genetic integrity of sugarcane germplasm in the USDA-ARS National Plant Germplasm System collection using single-dose SNP markers

“…These accessions originated from various geoclimatic regions and likely harbor genes for adaptation to different climatic stresses, pests, and diseases. Ample information on genetic diversity and population structure within this collection has been generated using molecular markers ( Brown et al., 2007 ; Nayak et al., 2014 ; Fickett et al., 2020 ; Xiong et al., 2022 ) and candidate genes ( Parco et al., 2017 ). Based on simple sequence repeat (SSR) genotyping results, a core collection including 300 accessions was proposed ( Nayak et al., 2014 ).…”

Analysis of the Genetic Diversity of Crops and Associated Microbiota

“…Genetic diversity characteristics were studied in the different germplasm collections of two crops of the Poaceae family, namely sugarcane (Saccharum spp.) [1] and rice (Oryza sativa L.) [2]), two horticultural crops, namely carrot (Daucus carota L.) [3] and turnip (Brassica rapa L.) [4], and the legume Bambara groundnut (Vigna subterranea (L.) Verdc.) [5].…”

“…The assessment of the genetic population structure and diversity plays a vital role in managing genetic resources and gene mapping. In one study [1], the genetic diversity and population structure among 196 Saccharum accessions were assessed, including 34 S. officinarum, 69 S. spontaneum, 17 S. robustum, 25 S. barberi, 13 S. sinense, 2 S. edule, and 36 Saccharum spp. hybrids.…”