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Title: High Density Genetic Maps of Seashore Paspalum Using Genotyping-By-Sequencing and Their Relationship to The Sorghum Bicolor Genome

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.

Authors:
 [1];  [2]; ORCiD logo [3]; ORCiD logo [4];  [5];  [1]
  1. Univ. of Georgia, Athens, GA (United States)
  2. Univ. of Georgia, Athens, GA (United States); Monsanto Company, Huxley, IA (United States)
  3. Univ. of Nebraska, Lincoln, NE (United States)
  4. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
  5. Univ. of Georgia, Griffin, GA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF)
OSTI Identifier:
1616088
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 9; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Qi, Peng, Eudy, Douglas, Schnable, James C., Schmutz, Jeremy, Raymer, Paul L., and Devos, Katrien M. High Density Genetic Maps of Seashore Paspalum Using Genotyping-By-Sequencing and Their Relationship to The Sorghum Bicolor Genome. United States: N. p., 2019. Web. https://doi.org/10.1038/s41598-019-48257-3.
Qi, Peng, Eudy, Douglas, Schnable, James C., Schmutz, Jeremy, Raymer, Paul L., & Devos, Katrien M. High Density Genetic Maps of Seashore Paspalum Using Genotyping-By-Sequencing and Their Relationship to The Sorghum Bicolor Genome. United States. https://doi.org/10.1038/s41598-019-48257-3
Qi, Peng, Eudy, Douglas, Schnable, James C., Schmutz, Jeremy, Raymer, Paul L., and Devos, Katrien M. Wed . "High Density Genetic Maps of Seashore Paspalum Using Genotyping-By-Sequencing and Their Relationship to The Sorghum Bicolor Genome". United States. https://doi.org/10.1038/s41598-019-48257-3. https://www.osti.gov/servlets/purl/1616088.
@article{osti_1616088,
title = {High Density Genetic Maps of Seashore Paspalum Using Genotyping-By-Sequencing and Their Relationship to The Sorghum Bicolor Genome},
author = {Qi, Peng and Eudy, Douglas and Schnable, James C. and Schmutz, Jeremy and Raymer, Paul L. and Devos, Katrien M.},
abstractNote = {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.},
doi = {10.1038/s41598-019-48257-3},
journal = {Scientific Reports},
number = 1,
volume = 9,
place = {United States},
year = {2019},
month = {8}
}

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Figures / Tables:

Table 1 Table 1: Marker number and length for the generated genetic maps.

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    Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.