Biology subjects

Quiroz-Chavez, J.

Publications and source records attributed to Quiroz-Chavez, J..

9 recordsLinked to original sources

bioRxiv2026

Chromosome-scale genome assembly of diploid halophyte Thinopyrum bessarabicum excludes J genome from polyploid Thinopyrum ancestry

Wild relatives of wheat harbour genetic diversity essential for improving resilience to climate-driven stresses, yet their deployment is hampered by unresolved evolutionary relationships and the absence of reference genomes. Here we present a chromosome-scale reference genome for Thinopyrum bessarabicum, a diploid halophyte and high-priority donor for wheat salt tolerance breeding. A key unresolved question is whether the diploid J genome contributed directly to the subgenome composition of extant polyploid Thinopyrum species, and which genomic features underpin its exceptional salt tolerance. Using this resource, we show that the diploid J genome of Th. bessarabicum is not represented among the subgenomes of polyploid Thinopyrum species, resolving a long-standing ambiguity in Triticeae genomics. Gene-level resolution of the reciprocal 4/5 chromosomal translocation across six related Triticeae species identifies conserved breakpoint gene pairs, supporting a single ancestral rearrangement. Genome-wide gene content analysis shows that halophytic capacity is underpinned by quantitative expansion of conserved stress-response gene families. Salt tolerance phenotyping validates chromosome 5J as a tolerance locus in both Th. bessarabicum and wheat introgression lines. A physically anchored marker framework and dual-reference skim-sequencing pipeline enable precise megabase-resolution characterisation of Th. bessarabicum introgressions in wheat, providing a genomic foundation for deploying J-genome diversity in crop improvement.

plant biology↗

bioRxiv2026

Natural and breeding selection converge on overlapping haplotypes with divergent directions and outcomes in wheat

Understanding how natural and breeding selection interact to shape crop genomes is essential for improving resilience under climate change. Here, we applied a k-mer-based, alignment-free haplotype assignment approach to whole-genome resequencing data from 827 wheat landraces representing seven geographic groups and 208 modern cultivars. We identified haplotypes associated with local adaptation that were enriched in specific agroecological regions, many of which were derived from wild-relative introgressions. Comparative analyses revealed that natural and breeding selection largely targeted overlapping haplotype sets, but often drove them in opposite directions. Notably, haplotypes conferring adaptive advantages were frequently associated with negative regulation of agronomic traits, explaining their reduced prevalence among breeding-selected haplotypes. These results reveal the genomic basis of trade-offs between environmental adaptation and productivity and offer a framework for exploiting adaptive diversity in wheat improvement.

plant biology↗

bioRxiv2025

KCFtools: Rapid alignment-free method for introgression screening and GWAS using k-mer profiles

MotivationIn the era of multiple genome references, researchers often align sequencing reads against distinct assemblies or even multiple references simultaneously. This enables applications such as the detection of introgressed segments or highly variable genomic regions, which are especially prevalent in large-genome crop species such as lettuce or wheat. However, these applications come at the cost of increased computational burden, inconsistencies in mapping methods, and reduced reproducibility across studies. To address these limitations, we developed KCFtools, a Java-based toolkit that identifies the presence and absence of k-mers in non-overlapping genomic or transcriptomic windows by comparing query and reference genomes. This alignment-free approach enables the efficient computation of an identity score for each window, thereby facilitating robust detection of introgressed or variable regions across genomes. ResultsWe systematically evaluated the performance and accuracy of the k-mer-based method implemented in KCFtools, benchmarking it against conventional SNP-based introgression detection pipelines. Our results demonstrate that KCFtools effectively captures introgressed segments and structurally diverse regions, even in species with fragmented or highly divergent reference genomes. In addition, we extended KCFtools to generate genotype matrices from k-mer variation tables. These matrices are compatible with Genome-Wide Association Studies (GWAS) software and allow the identification of loci associated with phenotypic traits. We showcase the utility of this approach by detecting known and novel associations for downy mildew resistance in lettuce, underscoring the pipelines potential for high-resolution, reference-agnostic population genetic analysis. Availabilityhttps://github.com/sivasubramanics/kcftools Contactc.s.sivasubramani@gmail.com

bioinformatics↗

bioRxiv2024

Population genomics uncover loci for trait improvement in the indigenous African cereal tef (Eragrostis tef)

Tef (Eragrostis tef) is an indigenous African cereal that is gaining global attention as a gluten-free "superfood" with high protein, mineral, and fibre contents. However, tef yields are limited by lodging and by losses during harvest owing its small grain size (150x lighter than wheat). Breeders must also consider a strong cultural preference for white-grained over brown-grained varieties. Tef is relatively understudied with limited "omics" resources. Here, we resequenced 220 tef accessions from an Ethiopian diversity collection and also conducted multi-locational phenotyping for 25 agronomic and grain traits. Grain metabolome profiling revealed differential accumulation of fatty acids and flavonoids between white and brown grains. We conducted k-mer and SNP-based genome wide association and uncovered novel marker-trait associations. A significant 70 kb peak for panicle morphology contained the tef orthologue of rice qSH1, a transcription factor regulating inflorescence morphology in cereals. We also observed a previously unknown relationship between grain size, colour, and fatty acids. These traits were highly associated with retrotransposon insertions in homoeologues of TRANSPARENT TESTA 2, a known regulator of grain colour. Our study provides valuable resources for tef research and breeding, facilitating the development of improved cultivars with desirable agronomic and nutritional properties.

genomics↗

bioRxiv2023

Origin and evolution of the bread wheat D genome

Bread wheat (Triticum aestivum) is a globally dominant crop and major source of calories and proteins for the human diet. Compared to its wild ancestors, modern bread wheat shows lower genetic diversity caused by polyploidisation, domestication, and breeding bottlenecks1,2. Wild wheat relatives represent genetic reservoirs, harbouring diversity and beneficial alleles that have not been incorporated into bread wheat. Here, we establish and analyse pangenome resources for Tauschs goatgrass, Aegilops tauschii, the donor of the bread wheat D genome. This new pangenome facilitated the cloning of a disease resistance gene and haplotype analysis across a complex disease resistance locus, allowing us to discern alleles from paralogous gene copies. We also reveal the complex genetic composition and history of the bread wheat D genome, involving previously unreported contributions from genetically and geographically discrete Ae. tauschii subpopulations. Together, our results reveal the complex history of the bread wheat D genome and demonstrate the potential of wild relatives in crop improvement.

genomics↗

bioRxiv2023

A population genomics approach to unlock the genetic potential of lablab (Lablab purpureus), an underutilized tropical forage crop

BackgroundIn Sub-Saharan Africa (SSA) livestock production and productivity are severely restricted by the scarce supply of feedstuffs and forage crops, while those available are often of low nutritional quality resulting in poor animal productivity and leading to widespread malnutrition among the public, particularly women and children. Traditionally, several tropical forage crops have been used in the region both in the rangelands and as cut-and-carry cropping systems, but limited research attention has been paid to improve the quality of and access to these animal feeds. Lablab (Lablab purpureus (L.) is one of the conventionally grown multi-purpose underutilized crops that originated in Africa. It is an annual or short-lived perennial multi-purpose forage legume which has versatile uses (as a vegetable and dry seed), and as feed for animals, or as green manure. To develop new and highly productive lablab varieties, using genomics-assisted selection, the present study aimed to identify quantitative trait loci (QTL) associated with agronomically important traits in lablab and to assess the stability of these traits across two different agro-ecologies in Ethiopia. ResultsOne hundred and forty-two cultivated and wild lablab accessions displayed significant agro-morphological variation in eight analysed traits, including plant height, total fresh weight, and total dry weight. Further, the agronomic performance of the accessions was significantly different across locations and years, highlighting the substantial genotype-by-environment interactions. The population genetic structure of the lablab accessions, based on half a million high quality single nucleotide polymorphisms (SNPs), revealed an independent domestication pattern for two-seeded and four-seeded lablab accessions. Furthermore, based on multi-environmental trial data, a genome-wide association study (GWAS) identified useful SNPs and k-mers for yield-related traits, such as plant height and total dry weight. ConclusionsGenomic-assisted breeding is playing a key role in accelerating trait improvement in temperate forages, such as perennial ryegrass and alfalfa. Here we show that a similar approach could benefit underutilized crops such as lablab. The publicly available genomic tools and field evaluation data from this study will offer a valuable resource for plant breeders and researchers, to initiate genomic-assisted breeding in lablab which will fast-track genetic gain per unit time and ultimately contribute towards achieving food/nutritional security in the region.

genomics↗

bioRxiv2023

Harnessing Landrace Diversity Empowers Wheat Breeding for Climate Resilience

Breeding crops resilient to climate change is urgently needed to help ensure food security. A key challenge is to harness genetic diversity to optimise adaptation, yield, stress resilience and nutrition. We examined the genetic and phenotypic diversity of the A.E. Watkins landrace collection of bread wheat (Triticum aestivum), a major global cereal, through whole-genome re-sequencing (827 Watkins landraces and 208 modern cultivars) and in-depth field evaluation spanning a decade. We discovered that modern cultivars are derived from just two of the seven ancestral groups of wheat, leaving five groups as previously untapped sources for breeding. This provides access to landrace-specific functional variations using structured germplasm, genotyping and informatics resources. Employing complementary genetic populations and approaches, we identified thousands of high-resolution quantitative trait loci (QTL) and significant marker-trait associations for major traits, revealing many Watkins-unique loci that can confer superior traits in modern wheat. Furthermore, we identified and functionally verified causative genes for climate-change adaptation, nutritional enhancement and resistance to wheat blast. Finally, we assessed the phenotypic effects of 44,338 Watkins-unique haplotypes, introgressed from 143 prioritised QTL in the context of modern cultivars, bridging the gap between landrace diversity and current breeding. This study establishes a framework for systematically utilising genetic diversity in crop improvement to achieve sustainable food security.

plant biology↗

bioRxiv2023

The wheat powdery mildew resistance gene Pm4 also confers resistance to wheat blast

Wheat blast, caused by the fungus Magnaporthe oryzae, threatens global cereal production since its emergence in Brazil in 1985 and recently spread to Bangladesh and Zambia. Here we demonstrate that the AVR-Rmg8 effector, common in wheat-infecting isolates, is recognised by the gene Pm4, previously shown to confer resistance to specific races of Blumeria graminis f.sp. tritici, the cause of powdery mildew of wheat. We show that Pm4 alleles differ in their recognition of different AVR-Rmg8 alleles, and some confer resistance only in seedling leaves but not spikes making it important to select for those alleles that function in both tissues. This study has identified a gene recognising an important virulence factor present in wheat blast isolates in Bangladesh and Zambia and represents an important first step towards developing durably resistant wheat cultivars for these regions.

plant biology↗

bioRxiv2021

Evolution of the bread wheat D-subgenome and enriching it with diversity from Aegilops tauschii

Aegilops tauschii, the diploid wild progenitor of the D-subgenome of bread wheat, constitutes a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. To better define and understand this diversity, we sequenced 242 Ae. tauschii accessions and compared them to the wheat D-subgenome. We characterized a rare, geographically-restricted lineage of Ae. tauschii and discovered that it contributed to the wheat D-subgenome, thereby elucidating the origin of bread wheat from at least two independent hybridizations. We then used k-mer-based association mapping to identify discrete genomic regions with candidate genes for disease and pest resistance and demonstrated their functional transfer into wheat by transgenesis and wide crossing, including the generation of a library of synthetic hexaploids incorporating diverse Ae. tauschii genomes. This pipeline permits rapid trait discovery in the diploid ancestor through to functional genetic validation in a hexaploid background amenable to breeding.

plant biology↗