SSR Marker-Assisted Management of Parental Germplasm in Sugarcane (Saccharum spp. hybrids) Breeding Programs

Abstract

Sugarcane (Saccharum spp. hybrids) is an important sugar and bioenergy crop with a high aneuploidy, complex genomes and extreme heterozygosity. A good understanding of genetic diversity and population structure among sugarcane parental lines is a prerequisite 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 accessions were analyzed with 21 fluorescence-labeled simple sequence repeats (SSR) markers and high-performance capillary electrophoresis (HPCE). A total of 226 SSR alleles of high-resolution capacity were identified. Among the series obtained from different origins, the YC-series, which contained eight unique alleles, had the highest genetic diversity. Based on the population structure analysis, the 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 clones introduced to China (including 28/29 CP-series accessions) while accessions native to China clustered in Pop2. The analysis of molecular variance (AMOVA), fixation index (Fst) value and gene flow (Nm) value all indicated the very low genetic differentiation between the two groups. This study illustrated that fluorescence-labeled SSR markers combined with high-performance capillary electrophoresis (HPCE) could be a very useful tool for genotyping of the polyploidy sugarcane. The results provided valuable information for sugarcane breeders to better manage the parental germplasm, choose the best parents to cross, and produce the best progeny to evaluate and select for new cultivar(s).

Registration of ‘YT 09‐13’ sugarcane

“…The nucleotide sequence of these SSR primers can be found in Wu et al. (2019). Based on a previous survey, the total number of SSR fragments/alleles produced by these 13 SSR primer pairs was 150 and the potential number of SSR fragments/alleles produced per SSR primer pair varied from 2 to 19 (Pan et al., 2007).…”

“…The molecular identity of YT 09-13 was defined with 150 DNA fragments/alleles amplifiable by 13 pairs of microsatellite (simple sequence repeat [SSR]) primers using a highthroughput procedure (Table 7) (Pan, Scheffler, & Richard, 2007). The nucleotide sequence of these SSR primers can be found in Wu et al (2019). Based on a previous survey, the total number of SSR fragments/alleles produced by these 13 SSR primer pairs was 150 and the potential number of SSR fragments/alleles produced per SSR primer pair varied from 2 to 19 (Pan et al, 2007).…”

Molecular Marker Technology for Crop Improvement

“…Marker-assisted selection was applied in four studies for (1) the selection of parental germplasm in sugarcane breeding programs [18], (2) improving blast resistance and salt tolerance in rice [19], (3) the selection of the pollination constant non-astringent (PCNA) type in Spanish germplasms of persimmon [20], and (4) the selection of resistance to plum pox virus (PPV) in apricot by allele-specific PCR [21]. Wu et al [18] identified two groups among the 150 most widely used sugarcane parental clones. Based on these results, the authors could identify the most appropriate cultivars to broaden the genetic base of breeding germplasm.…”

Molecular Marker Technology for Crop Improvement

“…Marker-assisted selection was applied in four studies for (1) the selection of parental germplasm in sugarcane breeding programs [18], (2) improving blast resistance and salt tolerance in rice [19], (3) the selection of the pollination constant non-astringent (PCNA) type in Spanish germplasms of persimmon [20], and (4) the selection of resistance to plum pox virus (PPV) in apricot by allele-specific PCR [21]. Wu et al [18] identified two groups among the 150 most widely used sugarcane parental clones. Based on these results, the authors could identify the most appropriate cultivars to broaden the genetic base of breeding germplasm.…”