Abstract
Achieving yield potential in chickpea (Cicer arietinum L.) is limited by many constraints that include biotic and abiotic stresses. Combining next-generation sequencing technology with advanced statistical modeling has the potential to increase genetic gain efficiently. Whole genome resequencing data was obtained from 315 advanced chickpea breeding lines from the Australian chickpea breeding program resulting in more than 298,000 single nucleotide polymorphisms (SNPs) discovered. Analysis of population structure revealed a distinct group of breeding lines with many alleles that are absent from recently released Australian cultivars. Genome-wide association studies (GWAS) using these Australian breeding lines identified 20 SNPs significantly associated with grain yield in multiple field environments. A reduced level of nucleotide diversity and extended linkage disequilibrium suggested that some regions in these chickpea genomes may have been through selective breeding for yield or other traits. A large introgression segment that introduced from C. echinospermum for phytophthora root rot resistance was identified on chromosome 6, yet it also has unintended consequences of reducing yield due to linkage drag. We further investigated the effect of genotype by environment interaction on genomic prediction of yield. We found that the training set had better prediction accuracy when phenotyped under conditions relevant to the targeted environments. We also investigated the effect of SNP functional annotation on prediction accuracy using different subsets of SNPs based on their genomic locations: regulatory regions, exome, and alternative splice sites. Compared with the whole SNP dataset, a subset of SNPs did not significantly decrease prediction accuracy for grain yield despite consisting of a smaller number of SNPs.
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Claims 8
Claim · model-written summary
Resequencing 315 chickpea breeding lines discovered more than 298,000 SNPs.
- Taxon
- chickpea
Cicer arietinume0 - Material
- advanced chickpea breeding linese0
- Outcome
- single nucleotide polymorphisms (SNPs) discoverede0
- Value
- more than 298,000e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Whole genome resequencing data was obtained from 315 advanced chickpea breeding lines from the Australian chickpea breeding program resulting in more than 298,000 single nucleotide polymorphisms (SNPs) discovered.”
Claim · model-written summary
Population structure revealed a distinct breeding-line group with alleles absent from recent Australian cultivars.
- Taxon
- chickpeaCicer arietinume1
- Outcome
- distinct group of breeding lines with many alleles that are absent from recently released Australian cultivarse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Analysis of population structure revealed a distinct group of breeding lines with many alleles that are absent from recently released Australian cultivars.”
e1“chickpea breeding lines”
Claim · model-written summary
GWAS identified 20 SNPs associated with chickpea grain yield across multiple field environments.
- Taxon
- chickpeaCicer arietinume1
- Gene
- SNPse0
- Outcome
- grain yielde0
- Value
- 20 SNPse0
- Setting
- multiple field environmentse0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Genome-wide association studies (GWAS) using these Australian breeding lines identified 20 SNPs significantly associated with grain yield in multiple field environments.”
e1“chickpea breeding lines”
Claim · model-written summary
Reduced nucleotide diversity and extended linkage disequilibrium suggested selection in some chickpea genomic regions.
- Taxon
- chickpeaCicer arietinume0
- Gene
- regions in these chickpea genomese0
- Outcome
- selective breeding for yield or other traitse0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“A reduced level of nucleotide diversity and extended linkage disequilibrium suggested that some regions in these chickpea genomes may have been through selective breeding for yield or other traits.”
Claim · model-written summary
A C. echinospermum introgression for phytophthora root rot resistance was identified on chromosome 6.
- Taxon
- C. echinospermumCicer echinospermume0
- Interactor
- phytophthora
Phytophthorae0pathogen - Gene
- chromosome 6e0
- Outcome
- large introgression segmente0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“A large introgression segment that introduced from C. echinospermum for phytophthora root rot resistance was identified on chromosome 6”
Claim · model-written summary
The chromosome 6 C. echinospermum introgression reduced chickpea yield through linkage drag.
- Taxon
- chickpeaCicer arietinume1
- Material
- C. echinospermume0
- Gene
- chromosome 6e0
- Outcome
- yielde0
- Direction
- reducinge0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“A large introgression segment that introduced from C. echinospermum for phytophthora root rot resistance was identified on chromosome 6, yet it also has unintended consequences of reducing yield due to linkage drag.”
e1“chickpea breeding lines”
Claim · model-written summary
Training sets phenotyped under conditions relevant to target environments had better yield prediction accuracy.
- Outcome
- prediction accuracye0
- Direction
- bettere0
- Qualifier
- conditions relevant to the targeted environmentse0
Not reportedComparatorValue
Verbatim
e0“We found that the training set had better prediction accuracy when phenotyped under conditions relevant to the targeted environments.”
Claim · model-written summary
Using SNP subsets based on functional annotation did not significantly decrease chickpea grain-yield prediction accuracy.
- Taxon
- chickpeaCicer arietinume1
- Outcome
- prediction accuracy for grain yielde0
- Direction
- did not significantly decreasee0
- Comparator
- whole SNP datasete0
Not reportedValue
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Compared with the whole SNP dataset, a subset of SNPs did not significantly decrease prediction accuracy for grain yield despite consisting of a smaller number of SNPs.”
e1“chickpea breeding lines”