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.
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Claims 8
Claim · model-written summary
The diversity panel contained many sequence variants identified by target enrichment sequencing.
- Outcome
- sequence variantse0
Not reportedTaxonComparatorValue
Verbatim
e0“By genotyping the diversity panel via target enrichment sequencing, we identified a large number of sequence variants.”
Claim · model-written summary
The study identified 217 nonredundant markers significantly associated with yield traits.
Not reportedTaxonDirection
Verbatim
e0“In total, 217 nonredundant markers and 225 candidate genes were identified to be significantly associated with the yield traits”
Claim · model-written summary
The study identified 225 candidate genes significantly associated with yield traits.
Not reportedTaxonDirection
Verbatim
e0“In total, 217 nonredundant markers and 225 candidate genes were identified to be significantly associated with the yield traits”
Claim · model-written summary
The panel had 282 characterized runs of homozygosity.
Not reportedTaxon
Verbatim
e0“We characterized 282 ROHs”
Claim · model-written summary
Runs of homozygosity occurred nonrandomly and were probably under selection.
Not reportedTaxonDirection
Verbatim
e0“the occurrence of ROHs in the genome were nonrandom and probably under selection”
Claim · model-written summary
High runs of homozygosity were associated with decreased total weight.
Not reportedTaxon
Verbatim
e0“The ROHs were associated with total weight and dry weight, and high ROHs resulted in a decrease in the two traits.”
Claim · model-written summary
High runs of homozygosity were associated with decreased dry weight.
Not reportedTaxon
Verbatim
e0“The ROHs were associated with total weight and dry weight, and high ROHs resulted in a decrease in the two traits.”
Claim · model-written summary
Genomic inbreeding was interpreted to harm sugarcane yield.
Verbatim
e0“genomic inbreeding has led to negative impacts on sugarcane yield”