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Title: Genome‐wide association study of multiple yield traits in a diversity panel of polyploid sugarcane ( Saccharum spp.)

Abstract

Abstract Sugarcane ( Saccharum spp.) is an important economic crop, contributing up to 80% of sugar and approximately 60% of biofuel globally. To meet the increased demand for sugar and biofuel supplies, it is critical to breed sugarcane cultivars with robust performance in yield traits. Therefore, dissection of causal DNA sequence variants is of great importance, as it provides genetic resources and fundamental information for crop improvement. In this study, we analyzed nine yield traits in a sugarcane diversity panel consisting of 308 accessions primarily selected from the World Collection of Sugarcane and Related Grasses. By genotyping the diversity panel via target enrichment sequencing, we identified a large number of sequence variants. Genome‐wide association studies between the markers and traits were conducted, taking dosages and gene actions into consideration. In total, 217 nonredundant markers and 225 candidate genes were identified to be significantly associated with the yield traits, which can serve as a comprehensive genetic resource database for future gene identification, characterization, and selection for sugarcane improvement. We further investigated runs of homozygosity (ROH) in the sugarcane diversity panel. We characterized 282 ROHs and found that the occurrence of ROHs in the genome were nonrandom and probably under selection. Themore » ROHs were associated with total weight and dry weight, and high ROHs resulted in a decrease in the two traits. This study suggests that genomic inbreeding has led to negative impacts on sugarcane yield.« less

Authors:
 [1];  [2];  [3];  [4]; ORCiD logo [2]
  1. Guangxi Key Lab for Sugarcane Biology Guangxi Univ. Nanning Guangxi 530005 China, Agronomy Department University of Florida Gainesville FL 32610 USA
  2. Agronomy Department University of Florida Gainesville FL 32610 USA
  3. Sugarcane Research Unit USDA‐ARS Houma LA 70360 USA
  4. Sugarcane Field Station USDA, ARS Canal Point FL 33438 USA
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1618175
Alternate Identifier(s):
OSTI ID: 1618177
Grant/Contract Number:  
DE‐SC0006995
Resource Type:
Published Article
Journal Name:
The Plant Genome
Additional Journal Information:
Journal Name: The Plant Genome Journal Volume: 13 Journal Issue: 1; Journal ID: ISSN 1940-3372
Publisher:
Wiley Blackwell (John Wiley & Sons)
Country of Publication:
United States
Language:
English

Citation Formats

Yang, Xiping, Luo, Ziliang, Todd, James, Sood, Sushma, and Wang, Jianping. Genome‐wide association study of multiple yield traits in a diversity panel of polyploid sugarcane ( Saccharum spp.). United States: N. p., 2020. Web. doi:10.1002/tpg2.20006.
Yang, Xiping, Luo, Ziliang, Todd, James, Sood, Sushma, & Wang, Jianping. Genome‐wide association study of multiple yield traits in a diversity panel of polyploid sugarcane ( Saccharum spp.). United States. https://doi.org/10.1002/tpg2.20006
Yang, Xiping, Luo, Ziliang, Todd, James, Sood, Sushma, and Wang, Jianping. Fri . "Genome‐wide association study of multiple yield traits in a diversity panel of polyploid sugarcane ( Saccharum spp.)". United States. https://doi.org/10.1002/tpg2.20006.
@article{osti_1618175,
title = {Genome‐wide association study of multiple yield traits in a diversity panel of polyploid sugarcane ( Saccharum spp.)},
author = {Yang, Xiping and Luo, Ziliang and Todd, James and Sood, Sushma and Wang, Jianping},
abstractNote = {Abstract Sugarcane ( Saccharum spp.) is an important economic crop, contributing up to 80% of sugar and approximately 60% of biofuel globally. To meet the increased demand for sugar and biofuel supplies, it is critical to breed sugarcane cultivars with robust performance in yield traits. Therefore, dissection of causal DNA sequence variants is of great importance, as it provides genetic resources and fundamental information for crop improvement. In this study, we analyzed nine yield traits in a sugarcane diversity panel consisting of 308 accessions primarily selected from the World Collection of Sugarcane and Related Grasses. By genotyping the diversity panel via target enrichment sequencing, we identified a large number of sequence variants. Genome‐wide association studies between the markers and traits were conducted, taking dosages and gene actions into consideration. In total, 217 nonredundant markers and 225 candidate genes were identified to be significantly associated with the yield traits, which can serve as a comprehensive genetic resource database for future gene identification, characterization, and selection for sugarcane improvement. We further investigated runs of homozygosity (ROH) in the sugarcane diversity panel. We characterized 282 ROHs and found that the occurrence of ROHs in the genome were nonrandom and probably under selection. The ROHs were associated with total weight and dry weight, and high ROHs resulted in a decrease in the two traits. This study suggests that genomic inbreeding has led to negative impacts on sugarcane yield.},
doi = {10.1002/tpg2.20006},
journal = {The Plant Genome},
number = 1,
volume = 13,
place = {United States},
year = {2020},
month = {3}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1002/tpg2.20006

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Cited by: 21 works
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