SSR Marker Development, Linkage Mapping, and QTL Analysis for Establishment Rate in Common Bermudagrass

Abstract

Common bermudagrass has been widely used as a major warmseason turf, forage, and soil stabilization grass in the southern United States. However, codominant marker development, linkage, and quantitative trait loci (QTL) mapping resources are limited in the important taxon. Accordingly, the objectives of this study were to develop simple sequence repeat (SSR) markers, construct a genetic map, and identify genomic regions associated with establishment rate. Five genomic SSR libraries were constructed, sequenced, and used in the development of 1003 validated SSR primer pairs (PPs). A linkage map was constructed using a first-generation selfed population derived from a genotype A12359 (2n = 4x = 36). A total of 249 polymorphic SSR PPs were mapped to 18 linkage groups (LGs). The total length of the map is 1094.7 cM, with an average marker interval of 4.3 cM. Ninety-eight out of 252 mapped loci (39%) were found to be distorted from the Mendelian 1:2:1 segregation ratio. Among the other 154 nondistorted loci, 88 coupling vs. 66 repulsion linkage phases were observed to confirm the allopolyploid origin of the parent. Ground coverage (GCR) phenotypic data in the establishment stage were collected in two replicated field trials. Quantitative trait loci mapping identified five genomic regions significantly related to the trait. The findings of this study provide valuable genetic tools and resources for genomic research, genetic improvement, and breeding new cultivars in the species.

Sequence-based genetic mapping of Cynodon dactylon Pers. reveals new insights into genome evolution in Poaceae

“…The filtered 7443 SNV markers and 266 SSRs from Guo et al 21 were used for LG construction. Markers with segregation distortion ( P < 0.01) were excluded during the framework LG construction.…”

“…Between the two S1 populations, the one derived from selfing of ‘A12359’ had less segregation distortion than that derived from ‘Zebra’. Consequently, the A12359 population was used for subsequent research including the development of an SSR marker-based genetic map 21 . All SSR markers showed disomic inheritance in the mapping population 21 .…”

“…Consequently, the A12359 population was used for subsequent research including the development of an SSR marker-based genetic map 21 . All SSR markers showed disomic inheritance in the mapping population 21 . Obviously, more research is needed to definitively reveal the genome constitution and subgenome differentiation of C. dactylon .…”

“…Previous genetic mapping research in C. dactylon has generated valuable information, yet a relatively small number of markers, specifically 291 loci in T89 19 and 252 loci in A12359 21 , have been mapped. Third-generation marker systems, such as genotyping-by-sequencing (GBS) can generate a large volume of single nucleotide variants (SNVs), which can be used to establish saturated genetic maps.…”

High-throughput SSR marker development and its application in a centipedegrass (Eremochloa ophiuroides (Munro) Hack.) genetic diversity analysis

“…Using transcriptome data resources, rapid progress in the development of SSR loci has been made in many green plant species [ 9 ]. Recently, a large amount of SSR markers were developed in forage and turfgrass crops such as perennial ryegrass [ 10 ], Italian ryegrass [ 11 ], alfalfa [ 12 ], hemarthria [ 13 ], red clover [ 14 ], orchardgrass [ 15 ], sudangrass [ 16 ], common bermudagrass [ 17 ], creeping bentgrass [ 18 ], seashore paspalum [ 19 ], and zoysiagrass [ 20 ]. To date, there is not a large quantity of SSR markers developed in centipedegrass, with the exception of a recent report on EST-SSR development from a cold-stressed transcriptome of centipedegrass [ 21 ].…”