Abstract
Hybrid potato breeding will transform the crop from a clonally propagated tetraploid to a seed-reproducing diploid. Historical accumulation of deleterious mutations in potato genomes has hindered the development of elite inbred lines and hybrids. Utilizing a whole-genome phylogeny of 92 Solanaceae and its sister clade species, we employ an evolutionary strategy to identify deleterious mutations. The deep phylogeny reveals the genome-wide landscape of highly constrained sites, comprising ∼2.4% of the genome. Based on a diploid potato diversity panel, we infer 367,499 deleterious variants, of which 50% occur at non-coding and 15% at synonymous sites. Counterintuitively, diploid lines with relatively high homozygous deleterious burden can be better starting material for inbred-line development, despite showing less vigorous growth. Inclusion of inferred deleterious mutations increases genomic-prediction accuracy for yield by 24.7%. Our study generates insights into the genome-wide incidence and properties of deleterious mutations and their far-reaching consequences for breeding.
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Claims 6
Claim · model-written summary
A whole-genome phylogeny of Solanaceae reveals highly constrained sites comprising about 2.4% of the genome.
- Taxon
- SolanaceaeSolanaceaee1
- Outcome
- highly constrained sitese0
- Value
- ∼2.4%e0
Verbatim
e0“The deep phylogeny reveals the genome-wide landscape of highly constrained sites, comprising ∼2.4% of the genome”
e1“a whole-genome phylogeny of 92 Solanaceae and its sister clade species”
Claim · model-written summary
Based on a diploid potato diversity panel, 367,499 deleterious variants were inferred.
- Taxon
- potato
Solanum tuberosume0 - Outcome
- deleterious variantse0
- Value
- 367,499e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Based on a diploid potato diversity panel, we infer 367,499 deleterious variants, of which 50% occur at non-coding and 15% at synonymous sites”
Claim · model-written summary
About 50% of the inferred deleterious variants in diploid potato occur at non-coding sites.
- Taxon
- potatoSolanum tuberosume0
- Outcome
- deleterious variantse0
- Value
- 50%e0
- Qualifier
- non-codinge0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Based on a diploid potato diversity panel, we infer 367,499 deleterious variants, of which 50% occur at non-coding and 15% at synonymous sites”
Claim · model-written summary
About 15% of the inferred deleterious variants in diploid potato occur at synonymous sites.
- Taxon
- potatoSolanum tuberosume0
- Outcome
- deleterious variantse0
- Value
- 15%e0
- Qualifier
- synonymous sitese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Based on a diploid potato diversity panel, we infer 367,499 deleterious variants, of which 50% occur at non-coding and 15% at synonymous sites”
Claim · model-written summary
Diploid potato lines with relatively high homozygous deleterious burden can be better starting material for inbred-line development despite less vigorous growth.
- Taxon
- potatoSolanum tuberosumt0
- Outcome
- starting material for inbred-line developmente0
- Qualifier
- despite showing less vigorous growthe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“potato”
e0“diploid lines with relatively high homozygous deleterious burden can be better starting material for inbred-line development, despite showing less vigorous growth”
Claim · model-written summary
Including inferred deleterious mutations increases genomic-prediction accuracy for yield by 24.7% in potato.
- Taxon
- potatoSolanum tuberosumt0
- Treatment
- Inclusion of inferred deleterious mutationse0
- Outcome
- genomic-prediction accuracy for yielde0
- Direction
- increasese0
- Value
- 24.7%e0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“potato”
e0“Inclusion of inferred deleterious mutations increases genomic-prediction accuracy for yield by 24.7%”
The same questions in other papers
loss of function · yield · Solanum tuberosum (potato)Positive and negative results
3 papers in the same direction as this paper · 6 in the opposite direction
- no effect
- negative
- negative
6 papers more in this group
See all 10 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.