Abstract
As a step towards trait mapping in the halophyte seashore paspalum (Paspalum vaginatum Sw.), we developed an F1 mapping population from a cross between two genetically diverse and heterozygous accessions, 509022 and HI33. Progeny were genotyped using a genotyping-by-sequencing (GBS) approach and sequence reads were analyzed for single nucleotide polymorphisms (SNPs) using the UGbS-Flex pipeline. More markers were identified that segregated in the maternal parent (HA maps) compared to the paternal parent (AH maps), suggesting that 509022 had overall higher levels of heterozygosity than HI33. We also generated maps that consisted of markers that were heterozygous in both parents (HH maps). The AH, HA and HH maps each comprised more than 1000 markers. Markers formed 10 linkage groups, corresponding to the ten seashore paspalum chromosomes. Comparative analyses showed that each seashore paspalum chromosome was syntenic to and highly colinear with a single sorghum chromosome. Four inversions were identified, two of which were sorghum-specific while the other two were likely specific to seashore paspalum. These high-density maps are the first available genetic maps for seashore paspalum. The maps will provide a valuable tool for plant breeders and others in the Paspalum community to identify traits of interest, including salt tolerance.
Highlights
As a step towards trait mapping in the halophyte seashore paspalum (Paspalum vaginatum Sw.), we developed an F1 mapping population from a cross between two genetically diverse and heterozygous accessions, 509022 and HI33
The ‘ASustacks’ derived reference set, filtered to include tags present in at least 50% of the samples, contained a total of 13,184 sequence tags. Using these reference tags and after all filtering and consolidation steps, a total of 4078 single nucleotide polymorphisms (SNPs) markers sequenced to a depth of ≥8X and with less than 20% of missing data was obtained for map construction
When the highly fragmented seashore paspalum genome was used as reference for SNP calling, 1885 HA, 1654
Summary
As a step towards trait mapping in the halophyte seashore paspalum (Paspalum vaginatum Sw.), we developed an F1 mapping population from a cross between two genetically diverse and heterozygous accessions, 509022 and HI33. The increased demand for food will necessitate expansion of crop cultivation into marginal areas that are already salt-affected or are vulnerable to salinization through seawater intrusion, storm surges and/or the salinizing effects of irrigation in arid areas[3] With these future challenges in mind, we have initiated research to understand the tolerance mechanisms in the halophytic species seashore paspalum (Paspalum vaginatum Sw.). Seashore paspalum is able to survive exposure to even ocean-strength levels of salt, and as such has become an important turf grass in coastal and salt-affected areas of the world[4] This panicoid grass is closely related to some of the world’s most important grain crops such as maize, sorghum and many of the millets, and may provide a gateway to improving these and other cereal crops for salt tolerance
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