Genetic diversity and population structure of Chinese natural bermudagrass [Cynodon dactylon (L.) Pers.] germplasm based on SRAP markers

Abstract

Bermudagrass [Cynodon dactylon (L.) Pers.], an important turfgrass used in public parks, home lawns, golf courses and sports fields, is widely distributed in China. In the present study, sequence-related amplified polymorphism (SRAP) markers were used to assess genetic diversity and population structure among 157 indigenous bermudagrass genotypes from 20 provinces in China. The application of 26 SRAP primer pairs produced 340 bands, of which 328 (96.58%) were polymorphic. The polymorphic information content (PIC) ranged from 0.36 to 0.49 with a mean of 0.44. Genetic distance coefficients among accessions ranged from 0.04 to 0.61, with an average of 0.32. The results of STRUCTURE analysis suggested that 157 bermudagrass accessions can be grouped into three subpopulations. Moreover, according to clustering based on the unweighted pair-group method of arithmetic averages (UPGMA), accessions were divided into three major clusters. The UPGMA dendrogram revealed that accessions from identical or adjacent areas were generally, but not entirely, clustered into the same cluster. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among accessions. Principal coordinate analysis (PCoA) with SRAP markers revealed a similar grouping of accessions to the UPGMA dendrogram and STRUCTUE analysis. Analysis of molecular variance (AMOVA) indicated that 18% of total molecular variance was attributed to diversity among subpopulations, while 82% of variance was associated with differences within subpopulations. Our study represents the most comprehensive investigation of the genetic diversity and population structure of bermudagrass in China to date, and provides valuable information for the germplasm collection, genetic improvement, and systematic utilization of bermudagrass.

Unraveling genetic variations of Dalbergia latifolia (Fabaceae) from Yogyakarta and Lombok Island, Indonesia

“…The average number of polymorphic bands is 13.6 per locus, a similar value (13.8) obtained by Zheng et al (2017) on Chinese bermudagrass (Cynodon dactylon) and this a little higher than the mean number of polymorphic loci reported for 152 studies of various plant species using SRAP (Robarts and Wolfe 2014), The moderate level of polymorphic loci (56%) obtained from this study suggesting that SRAP marker is considered reliable to detect polymorphism both at individual and population level. The values were generally lower than those obtained in other previous studies using more random markers such as RAPD, ISSR and SSR (Rout et al 2003;Bakshi and Sharma 2011;Cheng et al 2016;Zheng et al 2017). (Yulita and Rahmat 2019) considered SRAP and the other mentioned markers-e.g.…”

“…The scored data matrix was compiled in Excel software and used for further analyses. The polymorphic information content for each population and SRAP marker was following (Zheng et al 2017) a maximum of the value of Polymorphism Information Content (PIC) for dominant markers is 0.5 for f = 0.5 (Riek et al 2001). A cluster analysis was performed using UPGMA (Unweighted Pair Group Method with Arithmetic Average) (Sneath and Sokal 1973).…”

“…The SRAP marker was initially developed for gene tagging in Brassica oleracea L. (Li and Quiros 2001) to amplify specific coding regions of the genome targeting GC-rich exons and AT-rich promoters, introns, and spacers. Since then, the SRAP has been widely used to detect genetic variation at various taxonomic levels including population, such as bamboo (Zhu et al 2014), Cynodon dactylon (Zheng et al 2017 and Gonystylus bancanus (Yulita and Rahmat 2019), intra-specific hybrid detection in wheat (Liu et al 2008), Quantitative Trait Loci identification of Chrysanthemum (Zhang et al 2011), species complex of Festuca-Lolium (Cheng et al 2016), and mutant detection of Setaria italica (Yulita and Ridwan 2018). The results from this study will be used to provide insights into the genetic diversity within and among populations of D. latifolia that would be useful for the development of management strategies for ensuring long-term preservation and sustainable use of D. latifolia in Indonesia.…”

Genetic resources and genetic transformation in bermudagrass – a review

“…The later one demonstrated that C. arcuatus separated from another seven species, and the species had different chromosome numbers clustered in all instances, indicating a close relationship between 2x and 4x [27]. Since then, more and more molecular markers have been used in genetic diversity analysis of Cynodon accessions, such as AFLP, ISSR, RAPD, SRAP and SSR (details in Table 3) [28][29][30][31][32][33][34][35][36][37][38][39][40][41][42][43]. Khanal et al [44] successfully applied sugarcane EST-SSR analysing genetic diversity among triploid hybrids, tetraploid C. dactylon and diploid C. transvaalensis.…”

Interphase nuclear phenotype and chromosomal variation in Cynodon dactylon (L.) pers

“…This species is widely distributed in warm, humid and semi-arid areas around the Himalayas with excellent heat and drought tolerance capacity (Harlan et al 1970, Dunne et al 2019. This grass species is widely adapted to various environments of tropical and sub-tropical regions of the world and there are some ways for genetic diversity and population structure analysis of Bermudagrass (Zheng et al 2017). Bermuda grass has attracted interest of plant scientists because of their ease of cultivation, high forage production and high nutritional value (Pedreira 1996).…”