Abstract
BACKGROUND: Heterozygous genomes are widespread in outcrossing and clonally propagated crops. However, the variation in heterozygosity underlying key agronomic traits and crop domestication remains largely unknown. Cassava is a staple crop in Africa and other tropical regions and has a highly heterozygous genome. RESULTS: We describe a genomic variation map from 388 resequenced genomes of cassava cultivars and wild accessions. We identify 52 loci for 23 agronomic traits through a genome-wide association study. Eighteen allelic variations in heterozygosity for nine candidate genes are significantly associated with seven key agronomic traits. We detect 81 selective sweeps with decreasing heterozygosity and nucleotide diversity, harboring 548 genes, which are enriched in multiple biological processes including growth, development, hormone metabolisms and responses, and immune-related processes. Artificial selection for decreased heterozygosity has contributed to the domestication of the large starchy storage root of cassava. Selection for homozygous GG allele in MeTIR1 during domestication contributes to increased starch content. Selection of homozygous AA allele in MeAHL17 is associated with increased storage root weight and cassava bacterial blight (CBB) susceptibility. We have verified the positive roles of MeTIR1 in increasing starch content and MeAHL17 in resistance to CBB by transient overexpression and silencing analysis. The allelic combinations in MeTIR1 and MeAHL17 may result in high starch content and resistance to CBB. CONCLUSIONS: This study provides insights into allelic variation in heterozygosity associated with key agronomic traits and cassava domestication. It also offers valuable resources for the improvement of cassava and other highly heterozygous crops.
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Claims 12
Claim · model-written summary
The study produced a genomic variation map of 388 cassava genomes.
- Taxon
- cassava
Manihot esculentae0 - Outcome
- genomic variation mape0
- Value
- 388 resequenced genomese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“We describe a genomic variation map from 388 resequenced genomes of cassava cultivars and wild accessions.”
Claim · model-written summary
A genome-wide association study identified 52 loci for 23 agronomic traits.
- Taxon
- cassavaManihot esculentae1
- Outcome
- loci for 23 agronomic traitse0
- Value
- 52 locie0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“We identify 52 loci for 23 agronomic traits through a genome-wide association study.”
e1“Cassava is a staple crop”
Claim · model-written summary
Eighteen heterozygosity variants in nine candidate genes were significantly associated with seven traits.
- Taxon
- cassavaManihot esculentae1
- Gene
- candidate genese0
- Outcome
- seven key agronomic traitse0
- Direction
- associatede0
- Value
- Eighteen allelic variationse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Eighteen allelic variations in heterozygosity for nine candidate genes are significantly associated with seven key agronomic traits.”
e1“Cassava is a staple crop”
Claim · model-written summary
Eighty-one selective sweeps showed decreasing heterozygosity and nucleotide diversity and contained 548 genes.
- Taxon
- cassavaManihot esculentae1
- Outcome
- selective sweeps with decreasing heterozygosity and nucleotide diversitye0
- Value
- 81 selective sweepse0
- Qualifier
- 548 genese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“We detect 81 selective sweeps with decreasing heterozygosity and nucleotide diversity, harboring 548 genes”
e1“Cassava is a staple crop”
Claim · model-written summary
Genes in selective sweeps were enriched for growth, development, hormone and immune processes.
- Taxon
- cassavaManihot esculentae1
- Outcome
- enriched in multiple biological processese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“which are enriched in multiple biological processes including growth, development, hormone metabolisms and responses, and immune-related processes.”
e1“Cassava is a staple crop”
Claim · model-written summary
Selection for reduced heterozygosity contributed to domestication of the large starchy storage root.
- Taxon
- cassavaManihot esculentae0
- Outcome
- domestication of the large starchy storage roote0
- Qualifier
- decreased heterozygositye0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Artificial selection for decreased heterozygosity has contributed to the domestication of the large starchy storage root of cassava.”
Claim · model-written summary
Selection of the homozygous GG MeTIR1 allele increased starch content.
- Taxon
- cassavaManihot esculentae1
- Material
- homozygous GG allelee0
- Gene
- MeTIR1e0
- Outcome
- starch contente0
- Direction
- increasede0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Selection for homozygous GG allele in MeTIR1 during domestication contributes to increased starch content.”
e1“Cassava is a staple crop”
Claim · model-written summary
The homozygous AA MeAHL17 allele was associated with increased storage root weight.
- Taxon
- cassavaManihot esculentae0
- Material
- homozygous AA allelee0
- Gene
- MeAHL17e0
- Outcome
- storage root weighte0
- Direction
- increasede0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Selection of homozygous AA allele in MeAHL17 is associated with increased storage root weight and cassava bacterial blight (CBB) susceptibility.”
Claim · model-written summary
The homozygous AA MeAHL17 allele was associated with bacterial blight susceptibility.
- Taxon
- cassavaManihot esculentae0
- Material
- homozygous AA allelee0
- Gene
- MeAHL17e0
- Outcome
- cassava bacterial blight (CBB) susceptibilitye0
- Direction
- increasede0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Selection of homozygous AA allele in MeAHL17 is associated with increased storage root weight and cassava bacterial blight (CBB) susceptibility.”
Claim · model-written summary
Transient expression tests verified a positive role for MeTIR1 in starch content.
- Taxon
- cassavaManihot esculentae1
- Treatment
- transient overexpression and silencinge0
- Gene
- MeTIR1e0
- Outcome
- starch contente0
- Direction
- increasinge0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“We have verified the positive roles of MeTIR1 in increasing starch content and MeAHL17 in resistance to CBB by transient overexpression and silencing analysis.”
e1“Cassava is a staple crop”
Claim · model-written summary
Transient expression tests verified a positive role for MeAHL17 in CBB resistance.
- Taxon
- cassavaManihot esculentae1
- Treatment
- transient overexpression and silencinge0
- Gene
- MeAHL17e0
- Outcome
- resistance to CBBe0
- Direction
- positivee0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“We have verified the positive roles of MeTIR1 in increasing starch content and MeAHL17 in resistance to CBB by transient overexpression and silencing analysis.”
e1“Cassava is a staple crop”
Claim · model-written summary
MeTIR1 and MeAHL17 allele combinations may confer high starch content and CBB resistance.
- Taxon
- cassavaManihot esculentae1
- Gene
- MeTIR1 and MeAHL17e0
- Outcome
- high starch content and resistance to CBBe0
- Qualifier
- maye0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The allelic combinations in MeTIR1 and MeAHL17 may result in high starch content and resistance to CBB.”
e1“Cassava is a staple crop”
The same questions in other papers
loss of function · quality: sugar starch · Manihot esculenta (cassava)Positive and negative results
1 in the opposite direction
- negative
loss of function · disease · Manihot esculenta (cassava)Positive and negative results
5 papers in the same direction as this paper · 5 in the opposite direction
- positive
- negative
- negative
7 papers more in this group
See all 11 papers →Claims are grouped by organism, treatment and what was measured or targeted. A paper counts as positive when any of its claims in the group is positive.