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Title: A transcriptome-SNP-derived linkage map of Apios americana (potato bean) provides insights about genome re-organization and synteny conservation in the phaseoloid legumes

item SINGH, JUGPREET - Orise Fellow
item Kalberer, Scott
item BELAMKAR, VIKAS - University Of Nebraska
item ASSEFA, TESHALE - Orise Fellow
item NELSON, MATTHEW - Royal Botanical Gardens
item FARMER, ANDREW - National Center For Genome Resources
item BLACKMON, WILLIAM - Retired Non ARS Employee
item Cannon, Steven

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/10/2017
Publication Date: 10/25/2017
Citation: Singh, J., Kalberer, S.R., Belamkar, V., Assefa, T., Nelson, M.N., Farmer, A.D., Blackmon, W.J., Cannon, S.B. 2017. A transcriptome-SNP-derived linkage map of Apios americana (potato bean) provides insights about genome re-organization and synteny conservation in the phaseoloid legumes. Theoretical and Applied Genetics. 131(2):333-351.

Interpretive Summary: Squash and sunflower are the primary species native to North America that have been domesticated as crops. Another species that was widely used by Native Americans was Apios americana, or "potato bean" but this has received little attention as a modern crop. Nevertheless, Apios has several attractive features: it fixes nitrogen (producing a portion of its own fertilizer); it is high-protein; it produces palatable, potato-like tubers; it is flooding-tolerant; and it is well adapted to much of North America. This research paper reports the first genetic map for Apios, and uses the map to identify regions of the Apios genome (the set of chromosomes) that are conserved in several other legume crops: soybean, mung bean, adzuki bean, and common bean. The research will help researchers to more efficiently select for desirable Apios varieties, and is also helpful in understanding the genetic and evolutionary relationships between this important set of bean relatives.

Technical Abstract: 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 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 (SNP) 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 1,121 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 P. vulgaris and G. 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.