Genome architecture and tetrasomic inheritance of autotetraploid potato

Molecular Plant, Journal Year: 2022, Volume and Issue: 15(7), P. 1211 - 1226

Published: June 22, 2022

Potato (Solanum tuberosum) is the most consumed non-cereal food crop. Most commercial potato cultivars are autotetraploids with highly heterozygous genomes, severely hampering genetic analyses and improvement. By leveraging state-of-the-art sequencing technologies polyploid graph binning, we achieved a chromosome-scale, haplotype-resolved genome assembly of cultivated potato, Cooperation-88 (C88). Intra-haplotype comparative revealed extensive sequence expression differences in this tetraploid genome. We identified haplotype-specific pericentromeres on chromosomes, suggesting distinct evolutionary trajectory homologous centromeres. Furthermore, detected double reduction events that unevenly distributed haplotypes 1021 1034 selfing progeny, feature autopolyploid inheritance. distinguishing maternal paternal haplotype sets C88, simulated origin heterosis survey 3110 tetra-allelic loci deleterious mutations, which were masked condition by two parents. This study provides insights into genomic architecture autopolyploids will guide their breeding.

Language: Английский

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Unraveling the genetic architecture of blueberry fruit quality traits: major loci control organic acid content while more complex genetic mechanisms control texture and sugar content

BMC Plant Biology, Journal Year: 2025, Volume and Issue: 25(1)

Published: Jan. 10, 2025

Fruit quality traits, including taste, flavor, texture, and shelf-life, have emerged as important breeding priorities in blueberry (Vaccinium corymbosum). Organic acids sugars play crucial roles the perception of taste/flavor, where low high consumer liking are correlated with organic sugars, respectively. Blueberry texture appearance also critical for shelf-life consumers' willingness-to-pay. As genetic mechanisms that determine these fruit traits remain largely unknown, this study, an F1 mapping population was used to perform quantitative trait loci (QTL) pH, titratable acidity (TA), acids, total soluble solids (TSS), size, at harvest and/or post-storage weight loss. Twenty-eight QTLs were detected acidity-related parameters (pH, TA, acid content). Six citric acid, two quinic shikimic major effects consistently across years on same genomic regions chromosomes 3, 4, 5, Putative candidate genes identified using comparative transcriptomic analysis. No QTL malic content, TSS, or individual sugar content. A 146 minor texture- size-related parameters. With a few exceptions, generally inconsistent over post-storage, indicating highly nature. Our findings enhance understanding basis underlying guide future work exploit DNA-informed selection strategies programs. The major-effect characteristics could be potential targets develop DNA markers marker-assisted (MAS). On other hand, may more suitable approach than MAS when targeting size.

Language: Английский

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Identification of two mutant JASON-RELATED genes associated with unreduced pollen production in potato

Theoretical and Applied Genetics, Journal Year: 2024, Volume and Issue: 137(4)

Published: March 12, 2024

Abstract Key message Multiple QTLs control unreduced pollen production in potato. Two major-effect co-locate with mutant alleles of genes homology to AtJAS, a known regulator meiotic spindle orientation. In diploid potato the gametes (2 n ) rather than haploid ( number chromosomes has been widely reported. Besides their evolutionary important role sexual polyploidisation, also have practical value for breeding as bridge between and tetraploid germplasm. Although early articles argued monogenic recessive inheritance, genetic basis remained elusive. Here, three full-sib populations were genotyped an amplicon sequencing approach phenotyped across two growing seasons. We identified minor-effect regulating this trait. The largest effect displayed inheritance additive interaction. Both co-localised encoding putative AtJAS homologs, key meiosis II orientation Arabidopsis thaliana . function these candidate is consistent cytological phenotype mis-oriented metaphase plates observed parental clones. associated elevated levels showed deleterious mutation events: exonic transposon insert causing premature stop, amino acid change within highly conserved domain. Taken together, our findings shed light on natural variation underlying will facilitate interploidy by enabling marker-assisted selection

Language: Английский

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High-Density Linkage Map Constructed from a Skim Sequenced Diploid Potato Population Reveals Transmission Distortion and QTLs for Tuber Yield and Pollen Shed

Potato Research, Journal Year: 2023, Volume and Issue: 67(1), P. 139 - 163

Published: May 19, 2023

Abstract The reinvention of potato, from a tetraploid clonal crop into diploid seed-based hybrid crop, requires insight in the mutational load, recombination landscape, and genetic basis fertility. Genomics-based breeding QTL discovery rely on efficient genotyping strategies such as skim sequencing, to gather genotypic information. application sequencing full-sib population non-inbred parents remains challenging. Here, we report an R implementation OutcrossSeq pipeline for diploids. We applied this large sequenced potato population. used resulting bin-markers construction high-density parent specific linkage maps, highlighting variation parental rate structural variations. subsequently explored transmission ratio distortion non-independent assortment alleles, indicative large-effect deleterious mutations. Finally, identified QTLs seedling tuber yield pots pollen shed. This study showcases range analyses, marker inference, identification distortion, map mapping, new insights that contribute potato.

Language: Английский

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Local adaptation to climate facilitates a global invasion

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 17, 2024

Abstract Local adaptation may facilitate range expansion during invasions, but the mechanisms promoting destructive invasions remain unclear. Cheatgrass ( Bromus tectorum ), native to Eurasia and Africa, has invaded globally, with particularly severe impacts in western North America. We sequenced 307 genotypes conducted controlled experiments. found that diverse lineages America, where long-distance gene flow is common. Ancestry phenotypic clines predicted those range, indicating pre-adapted colonized different regions. Common gardens showed directional selection on flowering time reversed between warm cold sites, potentially maintaining clines. In Great Basin, genomic predictions of strong local identified sites cheatgrass most dominant. Preventing new introductions fuel critical for managing ongoing invasions.

Language: Английский

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QTL mapping of fruit quality traits in tetraploid kiwiberry (Actinidia arguta)

Horticultural Plant Journal, Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 1, 2024

Language: Английский

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Rose Rosette Disease Resistance Loci Detected in Two Interconnected Tetraploid Garden Rose Populations

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: July 7, 2022

Rose rosette disease (RRD), caused by the emaravirus (RRV), is a major threat to garden rose industry in United States. There has been limited work on genetics of host plant resistance RRV. Two interconnected tetraploid F1 biparental mapping populations were created develop high-quality linkage maps that allowed discovery RRD quantitative trait loci (QTLs) groups (LGs) 5, 6, and 7. These QTLs individually accounted for around 18-40% phenotypic variance. The locus with greatest effect partial was found LG 5. Most individuals 5 QTL simplex configuration; however, two duplex (likely due double reduction). Identification resistant regions interest can help development diagnostic markers marker-assisted selection breeding program.

Language: Английский

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Development of a 135K SNP genotyping array for Actinidia arguta and its applications for genetic mapping and QTL analysis in kiwifruit

Plant Biotechnology Journal, Journal Year: 2022, Volume and Issue: 21(2), P. 369 - 380

Published: Nov. 5, 2022

Summary Kiwifruit ( Actinidia spp) is a woody, perennial and deciduous vine. In this genus, there are multiple ploidy levels but the main cultivated cultivars polyploid. Despite availability of many genomic resources in kiwifruit, SNP genotyping still challenge given these different polyploidy. Recent advances array technologies have offered high‐throughput platform for genome‐wide DNA polymorphisms. study, we developed high‐density to facilitate genetic studies breeding applications kiwifruit. discovery was performed by sequencing 40 kiwifruit genotypes. The identified SNPs were stringently filtered sequence quality, predicted conversion performance distribution over available chinensis genome. A total 134 729 unique put on array. evaluated 400 individuals. We multidimensional scaling analysis assess diversity germplasm, showing that effective distinguish accessions. Using tetraploid F1 population, constructed an integrated linkage map covering 3060.9 cM across 29 groups QTL sex locus has been Linkage Group 3 (LG3) arguta . Finally, our dataset presented evidence tetrasomic inheritance with partial preferential pairing A. arguta. conclusion, 135K It advantage comprehensive design can be tool high‐value crop.

Language: Английский

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Dissecting the genetic basis of bioactive metabolites and fruit quality traits in blueberries (Vaccinium corymbosum L.)

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: Sept. 2, 2022

Blueberry is well-recognized as a healthy fruit with functionality derived largely from anthocyanin and chlorogenic acid. Despite their importance, no study to date has evaluated the genetic basis of these bioactives in blueberries relationship quality traits. Hence, fill this gap, mapping population including 196 F 1 individuals was phenotyped for acid concentration traits (titratable acidity, pH, total soluble solids) over 3 years data were used QTL correlation analysis. Total solids positively correlated glycosylated anthocyanin, respectively, indicating that parallel selection possible. Across all traits, 188 QTLs identified on chromosomes 1, 2, 4, 8, 9, 11 12. Notably, four major regions overlapping major-effect 4 responsible acylation glycosylation anthocyanins substrate sugar donor specific manner. Through comparative transcriptome analysis, multiple candidate genes QTLs, glucosyltransferases acyltransferases. Overall, provides first insights into controlling accumulation composition, establishes framework advance studies molecular breeding blueberry.

Language: Английский

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High-density linkage map construction in an autotetraploid blueberry population and detection of quantitative trait loci for anthocyanin content

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: Sept. 23, 2022

Highbush blueberry (Vaccinium corymbosum, 2n = 4x 48) is the most cultivated type of blueberry, both in New Zealand and overseas. Its perceived nutritional value conferred by phytonutrients, particularly anthocyanins. Identifying genetic mechanisms that control biosynthesis these metabolites would enable faster development cultivars with improved fruit qualities. Here, we used recently released tools for mapping autotetraploids to build a high-density linkage map highbush detect quantitative trait loci (QTLs) anthocyanin content. Genotyping was performed target sequencing, ∼18,000 single nucleotide polymorphism (SNP) markers being mapped into 12 phased groups (LGs). Fruits were harvested when ripe two seasons analyzed high-performance liquid chromatography-mass spectrometry (HPLC-MS): 25 different compounds identified quantified. Two major QTLs stable across years discovered, one on LG2 LG4, underlying candidate genes identified. Interestingly, presence anthocyanins containing acylated sugars appeared be under strong control. Information gained this study will design molecular marker-assisted selection help better understanding crop.

Language: Английский

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