A transcriptome-SNP-derived linkage map of Apios americana (potato bean) provides insights about genome re-organization and synteny conservation in the phaseoloid legumes
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 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 themore »
- Authors:
-
[2]
- US Dept. of Agriculture (USDA), Ames, IA (United States). Agricultural Research Service (ARS), Corn Insects and Crop Genetics Research Unit
- US Dept. of Agriculture (USDA), Ames, IA (United States). Agricultural Research Service (ARS), Corn Insects and Crop Genetics Research Unit, Crop Genome Informatics Lab.
- Univ. of Nebraska, Lincoln, NE (United States). Dept. of Agronomy and Horticulture
- Royal Botanic Gardens, West Sussex (United Kingdom)
- National Center for Genome Resources, Santa Fe, NM (United States)
- Mechanicsville, VA (United States)
- Publication Date:
- Research Org.:
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE; Agricultural Research Service (ARS); USDA
- OSTI Identifier:
- 1623593
- Grant/Contract Number:
- AC05-06OR23100
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Theoretical and Applied Genetics
- Additional Journal Information:
- Journal Volume: 131; Journal Issue: 2; Journal ID: ISSN 0040-5752
- Publisher:
- Springer Nature
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 54 ENVIRONMENTAL SCIENCES; Agriculture; Plant Sciences; Genetics & Heredity
Citation Formats
Singh, Jugpreet, Kalberer, Scott R., Belamkar, Vikas, Assefa, Teshale, Nelson, Matthew N., Farmer, Andrew D., Blackmon, William J., and Cannon, Steven B. A transcriptome-SNP-derived linkage map of Apios americana (potato bean) provides insights about genome re-organization and synteny conservation in the phaseoloid legumes. United States: N. p., 2017.
Web. doi:10.1007/s00122-017-3004-3.
Singh, Jugpreet, Kalberer, Scott R., Belamkar, Vikas, Assefa, Teshale, Nelson, Matthew N., Farmer, Andrew D., Blackmon, William J., & Cannon, Steven B. A transcriptome-SNP-derived linkage map of Apios americana (potato bean) provides insights about genome re-organization and synteny conservation in the phaseoloid legumes. United States. https://doi.org/10.1007/s00122-017-3004-3
Singh, Jugpreet, Kalberer, Scott R., Belamkar, Vikas, Assefa, Teshale, Nelson, Matthew N., Farmer, Andrew D., Blackmon, William J., and Cannon, Steven B. Wed .
"A transcriptome-SNP-derived linkage map of Apios americana (potato bean) provides insights about genome re-organization and synteny conservation in the phaseoloid legumes". United States. https://doi.org/10.1007/s00122-017-3004-3. https://www.osti.gov/servlets/purl/1623593.
@article{osti_1623593,
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},
author = {Singh, Jugpreet and Kalberer, Scott R. and Belamkar, Vikas and Assefa, Teshale and Nelson, Matthew N. and Farmer, Andrew D. and Blackmon, William J. and Cannon, Steven B.},
abstractNote = {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.},
doi = {10.1007/s00122-017-3004-3},
journal = {Theoretical and Applied Genetics},
number = 2,
volume = 131,
place = {United States},
year = {Wed Oct 25 00:00:00 EDT 2017},
month = {Wed Oct 25 00:00:00 EDT 2017}
}
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Figures / Tables:
Fig. 1: Flow chart describing various steps for reference transcriptome generation (A), validation (B), and single-nucleotide polymorphism (SNP) identification (C) in the F1 progeny and the parental breeding lines (BLs)
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