Biology subjects

Yates, S. A.

Publications and source records attributed to Yates, S. A..

6 recordsLinked to original sources

bioRxiv2026

Combing agronomic biofortification with a Zn-efficient wheat line synergistically increases grain Zn concentrations with varied effects on Cd in wheat grains

(Background and aims) Wheat grains are often too low in zinc (Zn) compared to human dietary needs, and are a major dietary source of highly toxic cadmium (Cd). Biofortification strategies can increase Zn in edible grain, but must not increase grain Cd. (Methods) We investigated the individual and combined effects of genetic and agronomic biofortification on Zn and Cd in wheat grains. Non-transgenic Bobwhite (BW-NT) and an OsNAS2-expressing line (BW-NAS) were grown in a pot experiment with isotope-labeled mineral Zn (70Zn) and green manure (70Zn, 106Cd). At flowering and maturity, Zn and Cd were quantified in wheat biomass. Wheat contents of Zn and Cd derived from inputs versus soil were determined using stable isotope analyses. (Results) Individually, the OsNAS2-expressing wheat and input application increased grain Zn. Combined OsNAS2 expression and input application led to grain concentrations of 76{+/-}4 mg kg-1 with mineral Zn application and 61{+/-}7 mg kg-1 with green manure. This was 154-217% higher than the 24{+/-}1 mg kg-1 observed in the BW-NT control and significantly higher than the additive effects of each strategy individually. The OsNAS2-expressing line increased grain Cd to 0.214{+/-}0.002 mg kg-1 under green manure, compared to 0.12{+/-}0.01 mg kg-1 in the BW-NT control. No other treatment increased grain Cd. (Conclusions) Our results encourage development of integrated genetic and agronomic biofortification strategies to increase grain Zn. They also underscore the need for careful monitoring of grain Cd concentrations when organic amendments are paired with genetic biofortification strategies.

plant biology↗

bioRxiv2023

High-resolution bulked segregant analysis enables candidate gene identification for bacterial wilt resistance in Italian ryegrass

Bacterial wilt, caused by Xanthomonas translucens pv. graminis (Xtg), is a serious disease of economically important forage grasses, including Italian ryegrass (Lolium multiflorum Lam.). A major QTL for resistance to Xtg was previously identified, but the precise location as well as the genetic factors underlying the resistance are yet to be determined. To this end, we applied a bulked segregant analysis (BSA) approach, using whole-genome deep sequencing of pools of the most resistant and most susceptible individuals of a large (n = 7,484) biparental F2 population segregating for resistance to Xtg. Using chromosome-level genome sequences as references, we were able to define a [~]300 kb region highly associated to resistance on pseudo-chromosome 4. Further investigation of this region revealed multiple genes with a known role in disease resistance, including genes encoding for Pik2-like disease resistance proteins, cysteine-rich kinases, and RGA4- and RGA5-like disease resistance proteins. Investigation of allele frequencies in the pools and comparative genome analysis in the grandparents of the F2 population revealed that some of these genes contain variants with allele frequencies that correspond to the expected heterozygosity in the resistant grandparent. This study emphasizes the efficacy combining BSA studies in very large populations with whole genome deep sequencing and high-quality genome sequences to pinpoint regions associated with a binary trait of interest and accurately define a small set of candidate genes. Furthermore, markers identified in this region hold significant potential for marker-assisted breeding strategies to breed resistance to Xtg in Italian ryegrass cultivars more efficiently.

plant biology↗

bioRxiv2021

GBSmode: a pipeline for haplotype-aware analysis of genotyping-by-sequencing data

2AO_SCPLOWBSTRACTC_SCPLOW2.1 BO_SCPLOWACKGROUNDC_SCPLOWGenotyping-by-sequencing (GBS) has revolutionised molecular genetic analysis. It enables simultaneous genotyping of thousands of DNA markers in the genome of any species. In contrast to whole-genome shotgun sequencing, GBS exploits a restriction enzyme to reduce genome complexity and directs the sequencing to begin at fixed digestion sites. However, currently used tools for the analysis of GBS data, such as SAMtools, often neglect the fundamental technical differences between GBS and shotgun sequencing. 2.2 RO_SCPLOWESULTSC_SCPLOWHere we present GBSmode, a dedicated pipeline to call DNA sequence variants using whole-read information from GBS data. It removes false positives by incorporating biological features such as the ploidy level and the number of possible alleles in the population under investigation. Comparison of GBSmode with SAMtools in an F2 population of rice (Oryza sativa L.) showed both identified a similar number of polymorphisms (13,449 and 14,445, respectively) with a high overlap (8,143). However, differences were found in the number of read misalignments (8.0% and 14.3% for GBSmode and SAMtools, respectively) and genotyping errors (5.0% and 8.3% for GBSmode and SAMtools, respectively). Further tests in a bi-parental F1 population of cassava (Manihot esculenta Crantz) showed GBSmode found 31,489 polymorphic loci, whereas the number was higher with SAMtools (43,860). However, this difference was mainly attributable to GBSmode rejecting 11,695 loci that were biologically not possible. 2.3 CO_SCPLOWONCLUSIONSC_SCPLOWThis study shows that GBSmode is a versatile tool for the analysis of GBS data. Moreover, GBSmode was able to reduce genotyping errors arising from read misalignments by combining haplotype data with biological information. Whilst other tools may find more markers, GBSmode is designed for accuracy.

bioinformatics↗

bioRxiv2021

Evidence for high intergenic sequence variation in heterozygous Italian ryegrass (Lolium multiflorum Lam.) genome revealed by a high-quality draft diploid genome assembly

BackgroundOver the last decade, progress in DNA sequencing technologies and assembly methods allowed plant scientists to move beyond the use of model organisms and work directly on the genomes of the major crops. Forage grass research can also benefit from this revolution, enabling progress in population genetic studies, functional biology, and genomics-assisted breeding. Due to its large genome size and high repeat content, so far only incomplete and fragmented assemblies are available for the grasses of the Lolium and Festuca species complex. FindingsHere, we report a highly contiguous draft assembly of Italian ryegrass (L. multiflorum Lam.), spanning 4.5 Gb and with a N50 of 3 Mb, containing ~70,000 gene models. Thanks to its relatedness to barley, 78% of the assembly was anchored on seven pseudomolecules. The high heterozygosity of the plant allowed obtaining a diploid assembly - i.e. across 95% of the assembly, both alleles were assembled on separate sequences. This feature allowed unraveling a very high amount of intergenic sequence variation between allelic sequences. ConclusionsWe present a nearly complete genome assembly of a genotype used in contemporary Swiss forage grass breeding programs. This work shows how genomic research has improved, allowing to decode the genetic code of large, complex, and heterozygous plants. It also allows the functional characterization of the ryegrass gene repertoire and the large-scale development of molecular markers. Furthermore, it paves the road for a reference-based characterization and exploitation of the genetic variation within the Lolium and Festuca species complex.

genomics↗

bioRxiv2020

Chromosome-scale de novo diploid assembly of the apple cultivar 'Gala Galaxy'

Apple (Malus x domestica) is one of the most important fruit crops in terms of worldwide production. Due to its self-incompatibility system and the long juvenile period, breeding of new apple cultivars combining traits desired by growers (e.g. yield, pest and disease resistance) and consumers (e.g. fruit size, color, and flavor) is a long and complex process. Genomics-assisted breeding strategies can facilitate the selection of germplasm leading to new cultivars. While the most complete apple genome assemblies available to date are from anther-derived homozygous lines, de novo assembly of apple genomes encompassing the natural heterozygosity remains challenging. Using long- and short-read sequencing technologies in combination with optical mapping, we de novo assembled a diploid and heterozygous genome of the apple cultivar Gala Galaxy. This approach resulted in 154 hybrid scaffolds (N50 = 34.3 Mb) spanning 999.9 Mb and in 414.7 Mb of unscaffolded sequences. Anchoring 31 scaffolds with a genetic map was sufficient to represent an entire haploid genome of 17 pseudomolecules (719.4 Mb). The remaining sequences were assembled in a second set of 17 pseudomolecules, which spanned 601 Mb, leaving 80.6 Mb of unplaced sequences. A total of 41,264 genes were annotated using 74,900 transcripts derived from RNA sequencing of pooled leaf tissue samples. This study provides a high-quality diploid reference genome sequence encompassing the natural heterozygosity of the widely popular cultivar Gala Galaxy. The DNA sequence resources and the assembly described here will serve as a solid foundation for fundamental and applied apple breeding research.

genomics↗

bioRxiv2018

Genetic determination of stomatal patterning in winter wheat (Triticum aestivum L.)

Leaf stomata are microscopic pores mediating plant-environment interactions. Their role in carbon uptake and transpiration make them prime candidates for improving water use efficiency (WUE). Stomatal density (SD), the number of stomata per unit area, has been shown to be negatively correlated with WUE. However, little is known about the genetic basis of SD in wheat (Triticum aestivum L.), and to what extant genetic variation exists in contemporary wheat germplasm. Here, we evaluated stomatal patterning over two growing seasons in a set of 333 wheat lines, representing the European winter wheat germplasm. Stomatal patterning was mainly determined by two underlying traits, the distance between files of stomata and the distance between stomata within a file. By haplotype association mapping, quantitative trait loci for SD were consistently detected in both seasons on wheat chromosomes (CHR) 2A, 3A and 7B. The single nucleotide polymorphism markers most significantly associated with SD coincided with the genes INDUCER OF CBF EXPRESSION 1 (ICE1) and STOMATAL CYTOKINESIS-DEFECTIVE 1 (SCD1) on CHR 3A, and genes involved in ethylene and auxin signaling on CHR 2A and 7B, respectively. Our study unlocks the phenotypic and genotypic variation for stomatal patterning traits in contemporary wheat germplasm. It provides gene targets for functional validation and practical tools to manipulate SD using marker-assisted selection for crop improvement.

plant biology↗