Abstract
Key messageWe report a linkage map for Apios americana and describe synteny with selected warm-season legumes. A translocation event in common bean and soybean is confirmed against Apios and Vigna species.Apios (Apios americana; “apios”), a tuberous perennial legume in the Phaseoleae tribe, was widely used as a food by Native Americans. Work in the last 40 years has led to several improved breeding lines. Aspects of the pollination biology (complex floral structure and tripping mechanism) have made controlled crosses difficult, and the previous reports indicated that the plant is likely primarily an outcrosser. We used a pseudo-testcross strategy to construct a genetic map specific to the maternal parent. The map was built using single-nucleotide polymorphism markers identified by comparing the expressed sequences of individuals in the mapping population against a de novo maternal reference transcriptome assembly. The apios map consists of 11 linkage groups and 1121 recombinationally distinct loci, covering ~ 938.6 cM. By sequencing the transcriptomes of all potential pollen parents, we were able to identify the probable pollen donors and to discover new aspects of the pollination biology in apios. No selfing was observed, but multiple pollen parents were seen within individual pods. Comparisons with genome sequences in other species in the Phaseoleae showed extended synteny for most apios linkage groups. This synteny supports the robustness of the map, and also sheds light on the history of the Phaseoleae, as apios is relatively early diverging in this tribe. We detected a translocation event that separates apios and two Vigna species from Phaseolus vulgaris and Glycine max. This apios mapping work provides a general protocol for sequencing-based construction of high-density linkage maps in outcrossing species with heterogeneous pollen parents.
Highlights
Molecular markers and genetic maps have been crucial in genetic diversity analysis and in speeding up the breeding efforts in many crops (Staub et al 1996; Xu and Crouch 2008; Dhillon et al 2009; Roy et al 2011; Jiang 2013; Belamkar et al 2016)
This study presents the development of a high-density single-nucleotide polymorphism (SNP) marker-based linkage map for apios
A comparison of apios transcriptome assembly against the fulllength coding sequences of related warm-season legumes P. vulgaris, G. max, V. radiata, and V. angularis revealed about 52–79% of corresponding matches (Table S1)
Summary
Molecular markers and genetic maps have been crucial in genetic diversity analysis and in speeding up the breeding efforts in many crops (Staub et al 1996; Xu and Crouch 2008; Dhillon et al 2009; Roy et al 2011; Jiang 2013; Belamkar et al 2016). Sequencing-based methods that combine discovery and genotyping in a single step are superseding conventional marker development techniques and have substantially reduced laboratory investments These methods can facilitate genome-wide identification of polymorphic markers in a cost-effective and timely fashion with or without the availability of previous genetic knowledge about a particular species. Whole-genome sequencing (Hillier et al 2008), exome capture (Ng et al 2009), RNA sequencing (Hansey et al 2012), and sequencing DNA fragments after digestion with various restriction enzymes (reviewed by Davey et al 2011) can produce thousands of polymorphic markers for genotyping and linkage analysis These techniques follow diverse protocols for variant detection and can be adopted in less-characterized species
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