Genome-Wide Association Study of Healthful Flavonoids among Diverse Mandarin Accessions

Mattia, Matthew R.; Du, Dongliang; Yu, Qibin; Kahn, Tracy L.; Roose, Mikeal L.; Hiraoka, Yoko; Wang, Yu; Muńoz, Patricio; Gmitter, Fred G.

doi:10.3390/plants11030317

Cited by 10 publications

(4 citation statements)

References 52 publications

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“…SNPs rates is directly proportional to the level of diversity, higher the number of SNPs greater the diversity among the citrus species, same as observed in other plants like rice (Terol et al 2008;Mattia et al 2022), Accordingly we hypothesized that the genetic variations reported in Citrus reticulata (present study) might be lower than that of Citrus sinensis, since Citrus reticulata is native to south Asia and most arose as crosses. Within a group such as satsumas there are many varieties that arose as mutants, but Citrus reticulata (broadly defined) includes many sexually produced hybrids.…”

Section: Discussionsupporting

confidence: 66%

Whole-Genome Sequencing and Variant Discovery ofCitrus reticulata‘Kinnow’ from Pakistan

Jabeen

Saif

Haq

et al. 2022

Preprint

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Citrus is a source of many nutritional and medicinal advantages, which is cultivated worldwide with major citrus groups of sweet oranges, mandarins, grapefruits, kumquats, lemons and limes. Pakistan produces all of its major citrus groups with mandarin (Citrus reticulata) being the prominent group that includes local commercial cultivars such as Feutral's Early, Dancy, Honey and Kinnow. The present study was designed to understand the genetic architecture of this unique variety of Citrus reticulata -'Kinnow'. The whole-genome resequencing and variant calling was performed to map the genomic variability that might be responsible for its particular characteristics like taste, seedlessness, juice content, thickness of peel and shelf-life. A total of 139,436,350 raw sequence reads using Illumina platform were generated with 20.9 Gb data in Fastq format having 98% effectiveness and 0.2% base call error rate. Overall, a total of 3,503,033 SNPs, 176,949 MNPs, 323,287 INS and 333,083 DEL were identified using the GATK4 variant calling pipeline against Citrus clementina as a reference genome. Further, g:Profiler bioinformatics tool was applied for annotating the newly found variants, harbor genes/transcripts and their involved pathways. A total of 73,864 transcripts harbors 4,336,352 variants, most of the observed variants were predicted in non-coding regions and 1,009 transcripts were found well annotated by different databases. Out of the total aforementioned transcripts, 588 involved in biological processes, 234 in molecular functions and 167 transcripts involved in cellular components in Citrus reticulata. In a nutshell, 18,153 high-impact variants and 216 genic-variants found in the current study which may be used for marker-assisted breeding programs of 'Kinnow' to identify this particular variety among others and to propagate its valued traits to improve the contemporary citrus varieties as well.

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Section: Discussionsupporting

confidence: 66%

Whole-Genome Sequencing and Variant Discovery ofCitrus reticulata‘Kinnow’ from Pakistan

Jabeen

Saif

Haq

et al. 2022

Preprint

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“…conducted GWAS analysis of genes responsible for flavonoid biosynthesis of diverse mandarin accessions. 46 Another study by Minamikawa et al. used GWAS analysis to identify putative genetic traits controlling fruit quality.…”

Section: Discussionmentioning

confidence: 99%

Citrus genomic resources unravel putative genetic determinants of Huanglongbing pathogenicity

Gao¹,

Xu²,

Li³

et al. 2023

iScience

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“…The large amount of whole genome sequencing data of citrus and relatives enabled GWAS analysis of putative genetic determinants of HLB resistance/tolerance and susceptibility. Mattia and colleagues conducted GWAS analysis of genes responsible for flavonoid biosynthesis of diverse mandarin accessions (Mattia et al, 2022). Another study by Minamikawa et al .…”

Section: Discussionmentioning

confidence: 99%

Citrus genomic resources unravel putative genetic determinants of Huanglongbing, a pathogen-triggered immune disease

Gao

et al. 2022

Preprint

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Citrus is one of the most important tree crops worldwide and citrus production is threatened by Huanglongbing (HLB), a devasting citrus disease caused by Candidatus Liberibacter. HLB is a pathogen-triggered immune disease, in which the pathogen initiates systemic and chronic immune responses including the excessive production of reactive oxidative species, which subsequently lead to cell death of phloem tissues and HLB disease symptoms. Here, we identified putative genetic determinants of HLB pathogenicity by integrating citrus genomic resources to characterize the pan-genome of accessions that differ in their response to HLB. Genome-wide association mapping and analysis of allele-specific expression between susceptible, tolerant, and resistant accessions further refined candidates underlying the response to HLB. To enable these analyses we first developed a phased diploid assembly of Citrus sinensis Newhall genome and produced resequencing data for 91 citrus accessions that differ in their response to HLB. These data were combined with previous resequencing data from 356 sequenced accessions for genome-wide association mapping of the HLB response. Genes with HLB pathogenicity were associated with the host immune response, ROS production, and antioxidants. Overall, this study has provided a significant recourse of citrus genomic data and we have identified candidate genes to be further explored to understand the genetic determinants of HLB pathogenicity and to generate HLB resistant/tolerant citrus varieties.

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Genome-Wide Association Study of Healthful Flavonoids among Diverse Mandarin Accessions

Cited by 10 publications

References 52 publications

Whole-Genome Sequencing and Variant Discovery ofCitrus reticulata‘Kinnow’ from Pakistan

Whole-Genome Sequencing and Variant Discovery ofCitrus reticulata‘Kinnow’ from Pakistan

Citrus genomic resources unravel putative genetic determinants of Huanglongbing pathogenicity

Citrus genomic resources unravel putative genetic determinants of Huanglongbing, a pathogen-triggered immune disease

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