Genome-wide presence/absence variation discovery and its application in Peach (Prunus persica)

Bie, Haiying; Li, Yong; Zhao, Yuwu; Fang, Weichao; Chen, Chang-Wen; Wang, Xinwei; Wu, Jinlong; Wang, Lirong; Cao, Ke

doi:10.1016/j.plantsci.2023.111778

Cited by 3 publications

(1 citation statement)

References 60 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In our study, PAV analyses revealed the loss of 5074 NAC genes during sunflower domestication and improvement, consistent with the trend found in sunflower domestication [ 25 ]. PAV is an important contributor to the studies of genetic diversity, gene identification, and molecular marker development in plants [ 66 ]. Understanding the PAV gene could support crop improvement applications and potentially reintroduce the gene into modern varieties [ 67 ].…”

Section: Discussionmentioning

confidence: 99%

Pangenome characterization and analysis of the NAC gene family reveals genes for Sclerotinia sclerotiorum resistance in sunflower (Helianthus annuus)

Lu,

Liu,

Kong

et al. 2024

BMC Genom Data

View full text Add to dashboard Cite

Background Sunflower (Helianthusannuus) is one of the most important economic crops in oilseed production worldwide. The different cultivars exhibit variability in their resistance genes. The NAC transcription factor (TF) family plays diverse roles in plant development and stress responses. With the completion of the H. annuus genome sequence, the entire complement of genes coding for NACs has been identified. However, the reference genome of a single individual cannot cover all the genetic information of the species. Results Considering only a single reference genome to study gene families will miss many meaningful genes. A pangenome-wide survey and characterization of the NAC genes in sunflower species were conducted. In total, 139 HaNAC genes are identified, of which 114 are core and 25 are variable. Phylogenetic analysis of sunflower NAC proteins categorizes these proteins into 16 subgroups. 138 HaNACs are randomly distributed on 17 chromosomes. SNP-based haplotype analysis shows haplotype diversity of the HaNAC genes in wild accessions is richer than in landraces and modern cultivars. Ten HaNAC genes in the basal stalk rot (BSR) resistance quantitative trait loci (QTL) are found. A total of 26 HaNAC genes are differentially expressed in response to Sclerotinia head rot (SHR). A total of 137 HaNAC genes are annotated in Gene Ontology (GO) and are classified into 24 functional groups. GO functional enrichment analysis reveals that HaNAC genes are involved in various functions of the biological process. Conclusions We identified NAC genes in H. annuus (HaNAC) on a pangenome-wide scale and analyzed S. sclerotiorum resistance-related NACs. This study provided a theoretical basis for further genomic improvement targeting resistance-related NAC genes in sunflowers.

show abstract

Section: Discussionmentioning

confidence: 99%

Pangenome characterization and analysis of the NAC gene family reveals genes for Sclerotinia sclerotiorum resistance in sunflower (Helianthus annuus)

Lu,

Liu,

Kong

et al. 2024

BMC Genom Data

View full text Add to dashboard Cite

show abstract

Historic breeding practices contribute to germplasm divergence in leaf specialized metabolism and ecophysiology in cultivated sunflower (Helianthus annuus)

Dowell,

Bowsher,

Jamshad

et al. 2024

American J of Botany

View full text Add to dashboard Cite

PremiseThe use of hybrid breeding systems to increase crop yields has been the cornerstone of modern agriculture and is exemplified in the breeding and improvement of cultivated sunflower (Helianthus annuus). However, it is poorly understood what effect supporting separate breeding pools in such systems, combined with continued selection for yield, may have on leaf ecophysiology and specialized metabolite variation.MethodsWe analyzed 288 lines of cultivated H. annuus to examine the genomic basis of several specialized metabolites and agronomically important traits across major heterotic groups.ResultsHeterotic group identity supports phenotypic divergences between fertility restoring and cytoplasmic male‐sterility maintainer lines in leaf ecophysiology and specialized metabolism. However, the divergence is not associated with physical linkage to nuclear genes that support current hybrid breeding practices in cultivated H. annuus. Additionally, we identified four genomic regions associated with leaf ecophysiology and specialized metabolism that colocalize with previously identified QTLs for quantitative self‐compatibility traits and with S‐protein homolog (SPH) proteins, a recently discovered family of proteins associated with self‐incompatibility and self/nonself recognition in Papaver rhoeas (common poppy) with suggested conserved downstream mechanisms among eudicots.ConclusionsFurther work is necessary to confirm the self‐incompatibility mechanisms in cultivated H. annuus and their relationship to the integrative and polygenic architecture of leaf ecophysiology and specialized metabolism in cultivated sunflower. However, because self‐compatibility is a derived quantitative trait in cultivated H. annuus, trait linkage to divergent phenotypic traits may have partially arisen as a potential unintended consequence of historical breeding practices and selection for yield.

show abstract

Historic breeding practices contribute to germplasm divergence in leaf specialized metabolism and ecophysiology in cultivated sunflower (Helianthus annuus)

Dowell,

Bowsher,

Jamshad

et al. 2024

Preprint

View full text Add to dashboard Cite

The use of hybrid breeding systems to increase crop yields has been the cornerstone of modern agriculture and is exemplified in the breeding and improvement of cultivated sunflower (Helianthus annuus). However, it is poorly understood what effect supporting separate breeding pools in such systems, combined with continued selection for yield, may have on leaf ecophysiology and specialized metabolite variation. Here, we analyze 288 cultivated H. annuus lines to examine the genomic basis of several specialized metabolites and agronomically important traits across major heterotic groups. Heterotic group identity supports phenotypic divergences between fertility restoring and cytoplasmic male-sterility maintainer lines in leaf ecophysiology and specialized metabolism. However, the divergence is not associated with physical linkage to nuclear genes that support current hybrid breeding systems in cultivated H. annuus. Further, we identified four genomic regions associated with variation in leaf ecophysiology and specialized metabolism that co-localize with previously identified QTLs in cultivated H. annuus for quantitative self-compatibility traits and with SPH-proteins, a recently discovered family of proteins associated with self-incompatibility and self/nonself recognition in Papaver rhoeas (common poppy) with suggested conserved downstream mechanisms among eudicots. Self-compatibility is a derived trait in cultivated H. annuus with quantitative variation in selfing success, suggesting that trait linkage to divergent phenotypic traits may have partially arisen as a potential unintended consequence of historical breeding practices. Further work is necessary to confirm the self-incompatibility mechanisms in cultivated H. annuus and their relationship to the integrative and polygenic architecture of leaf ecophysiology and specialized metabolism in cultivated sunflower.

show abstract

Genome-wide presence/absence variation discovery and its application in Peach (Prunus persica)

Cited by 3 publications

References 60 publications

Pangenome characterization and analysis of the NAC gene family reveals genes for Sclerotinia sclerotiorum resistance in sunflower (Helianthus annuus)

Pangenome characterization and analysis of the NAC gene family reveals genes for Sclerotinia sclerotiorum resistance in sunflower (Helianthus annuus)

Historic breeding practices contribute to germplasm divergence in leaf specialized metabolism and ecophysiology in cultivated sunflower (Helianthus annuus)

Historic breeding practices contribute to germplasm divergence in leaf specialized metabolism and ecophysiology in cultivated sunflower (Helianthus annuus)

Contact Info

Product

Resources

About