Biology subjects

Ben-David, R.

Publications and source records attributed to Ben-David, R..

6 recordsLinked to original sources

bioRxiv2024

Whole-Genome Sequencing of the Wild Barley Diversity Collection: A Resource for Identifying and Exploiting Genetic Variation for Cultivated Barley Improvement

To exploit allelic variation in Hordeum vulgare subsp. spontaneum, the Wild Barley Diversity Collection was evaluated for several agronomic traits and subjected to paired-end Illumina sequencing at [~]9X depth, generating 109.5 million single nucleotide polymorphisms after alignment to the Morex V3 assembly. A genome-wide association study of lemma color identified one marker-trait association (MTA) on chromosome 1HL close to HvBlp, the cloned gene controlling black lemma. Four MTAs were identified for stem rust resistance: one co-locating to the complex RMRL1-RMRL2 locus on 5HL, and three novel loci on 1HS, 1HL, and 5HL. Six MTAs for days to heading (DTH) on vernalized plants were identified on all chromosomes except 1H and 6H. Two MTAs for DTH on non-vernalized plants were identified on chromosomes 1HL and 2HS. All MTAs for DTH were novel. The whole genome sequence data described herein will facilitate the identification and utilization of new alleles for barley improvement.

genomics↗

bioRxiv2024

Population genomics and molecular epidemiology of wheat powdery mildew in Europe

Agricultural diseases are a major threat to sustainable food production. Yet, for many pathogens we know exceptionally little about their epidemiological and population dynamics, and this knowledge gap is slowing the development of efficient control strategies. Here we study the population genomics and molecular epidemiology of wheat powdery mildew, a disease caused by the biotrophic fungus Blumeria graminis forma specialis tritici (Bgt). We sampled Bgt for two consecutive years, 2022 and 2023, from 22 countries in Europe and surrounding regions, and compiled a genomic dataset of 415 Bgt isolates. We found one single epidemic unit in the north of Europe, consisting of a highly homogeneous population. Conversely, the south of Europe hosts smaller local populations which are less interconnected. In addition, we show that the population structure can be largely predicted by the prevalent wind patterns. We identified several loci that were under selection in the recent past, including fungicide targets and avirulence genes. Some of these loci are common between populations, while others are not, suggesting different local selective pressures. We reconstructed the evolutionary history of one of these loci, AvrPm17, coding for an effector recognized by the wheat receptor Pm17. We found evidence for a soft sweep on standing genetic variation. Multiple AvrPm17 haplotypes, which can partially escape recognition by Pm17, spread rapidly throughout the continent upon its introduction in the early 2000s. We also identified a new virulent variant, which emerged more recently and can evade Pm17 resistance altogether. Overall, we highlight the potential of genomic surveillance in resolving the evolutionary and epidemiological dynamics of agricultural pathogens, as well as in guiding control strategies.

evolutionary biology↗

bioRxiv2023

Pre-anthesis spike growth dynamics and its association to yield components among elite bread wheat cultivars (Triticum aestivum L. spp.) under Mediterranean climate

Wheat (Triticum spp.) grain yield (GY) is highly associated with grain number per unit area (GN m-2). Biomass accumulation and partitioning are essential to understand pre-anthesis spike growth dynamics which determines spike dry matter at anthesis (SDMa) - a GN determinant. Spike growth takes place during the stem elongation period (SE), from terminal spikelet to anthesis, following leaf and spikelet initiation (LS) from sowing to terminal spikelet. In this study, bread wheat cultivars were examined under Mediterranean semi-arid conditions to determine (i) the varietal differences in pre-anthesis phase duration, (ii) whether this variability influences biomass partitioning and spike-related traits, and (iii) to what extent, the genotypic variations in pre-anthesis phase duration and spike growth are associated with yield components. A panel of Israeli commercial bread wheat cultivars were grown in the field during 2016-17 (three environments) and 2017-18 (two environments) and characterized for pre-anthesis phases, floral conditions and spike fertility via histological measurements, spike traits and dry matter accumulation and partitioning at anthesis and maturity and for yield components. Significant variability in the timing of pre-anthesis phases was detected within the tested panel. LS duration, and occasionally SE, favourably related with a better dry matter of fertile florets spike-1 (at anthesis) and SDM (at both anthesis and maturity). Two cultivar pairs Zahir-Yuval and Negev-Gedera, which flowered concurrently, revealed significant differences in the durations of LS and SE phases across the environments. Longer LS (e.g., in cultivars Zahir and Negev) exhibited increased spikelets number spike-1, whereas longer SE (e.g., in Yuval and Gedera) enhanced spike fertility through improving the survival rate of floret primordia (FSR%) of central spikelets. However, there was a trade-off for FSR at the proximal and distal spike portions, resulting reduction of final GN (or GY) in cultivars with longer SE. It is concluded that, in this panel, the duration of both LS and SE contribute to spike fertility. However, under short wheat growing cycle, LS duration seemed a stronger driver than SE for GN and yield enhancement. These highlights the novel importance of pre-anthesis phases, especially the role of LS in wheat yield increment during the short growing cycle. The varietal combination with variable LS and SE duration could be implemented in the breeding pipeline and used as pre-breeding materials for GN improvement. Furthermore, the findings will improve pre-anthesis traits adoption in Mediterranean bread wheat future breeding programs.

plant biology↗

bioRxiv2022

Long-read genome sequencing accelerated the cloning of Pm69 by resolving the complexity of a rapidly evolving resistance gene cluster in wheat

Gene cloning in repeat-rich polyploid genomes remains challenging. Here we describe a strategy for overcoming major bottlenecks in the cloning of the powdery mildew (Pm) resistance gene (R-gene) Pm69 derived from tetraploid wild emmer wheat (WEW). A conventional positional cloning approach encountered suppressed recombination due to structural variations, while chromosome sorting yielded an insufficient purity level. A Pm69 physical map, constructed by assembling ONT long-read genome sequences, revealed a rapidly evolving nucleotide-binding leucine-rich repeat (NLR) R-gene cluster. A single candidate NLR was identified within this cluster by anchoring RNASeq reads of susceptible mutants to ONT contigs and was validated by the virus-induced gene silencing (VIGS) approach. Pm69, comprising Rx_N with RanGAP interaction sites, NB-ARC, and LRR domains, is probably a newly evolved NLR discovered only in one location across the WEW distribution range in the Fertile Crescent. Pm69 was successfully introgressed into durum and bread wheat, and a diagnostic molecular marker could be used to accelerate its deployment and pyramiding with other resistance genes.

genetics↗

bioRxiv2020

Genetic improvement of wheat early vigor promote weed-competitiveness under Mediterranean climate

Chemical weed-control is the most effective practice for wheat, however, rapid evolution of herbicide-resistant weeds threat food-security and calls for integration of non-chemical practices. We hypothesis that integration of GAR dwarfing-genes into elite wheat cultivars can promote early vigor and weed-competitiveness under Mediterranean climate. We develop near-isogenic lines of bread wheat cultivars with GAR dwarfing genes and evaluate them for early vigor and weed-competitiveness under various environmental and management conditions to identify promising NIL for weed-competitiveness and grain yield. While all three NILs, OC1 (Rht8,12), ZC4 (Rht12,13), and BNMF12 (Rht12), responded to gibberellic acid, they exhibited differences in early vigor. Greenhouse and field evaluation highlighted OC1 as a promising line, with significant advantage in early vigor over its parental. To facilitate accurate and continuous early vigor data collection, we applied non-destructive image-based phenotyping approaches which offers non-expensive and end-user friendly solution for selection. NIL OC1 was tested under different weed density level, infestation waves, and temperatures and highlight the complex genotypic x environmental x management interactions. Our findings demonstrate the potential of genetic modification of dwarfing genes as promising approach to improve weed-competitiveness, and serve as basis for future breeding efforts to support sustainable wheat production under semi-arid Mediterranean climate.

plant biology↗

bioRxiv2018

Genome based QTL and meta-QTL analyses of thousand-kernel weight in tetraploid wheat

The domestication and subsequent genetic improvement of wheat led to the development of large-seeded cultivated wheat species relative to their smaller-seeded wild progenitors. While increased grain weight (GW) continues to be an important goal of many wheat breeding programs, few genes underlying this trait have been identified despite an abundance of studies reporting quantitative trait loci (QTLs) for GW. Here we perform a QTL analysis for GW using a population of recombinant inbred lines (RILs) derived from the cross between wild emmer wheat accession Zavitan and durum wheat variety Svevo. Identified QTLs in this population were anchored to the recent Zavitan reference genome, along with previously published QTLs for GW in tetraploid wheat. This genome-based, meta-QTL analysis enabled the identification of a locus on chromosome 6A whose introgression from wild wheat positively affects GW. The locus was validated using an introgression line carrying the 6A GW QTL region from Zavitan in a Svevo background, resulting in >8% increase in GW compared to Svevo. Using the reference sequence for the 6A QTL region, we identified a wheat ortholog to OsGRF4, a rice gene previously associated with GW. The coding sequence of this gene (TtGRF4-A) contains four SNPs between Zavitan and Svevo, one of which reveals the Zavitan allele to be rare in a core collection of wild emmer and completely absent from the domesticated emmer genepool. Similarly, another wild emmer accession (G18-16) was found to carry a rare allele of TtGRF4-A that also positively affects GW and is characterized by a unique SNP absent from the entire core collection. These results exemplify the rich genetic diversity of wild wheat, posit TtGRF4-A as a candidate gene underlying the 6A GW QTL, and suggest that the natural Zavitan and G18-16 alleles of TtGRF4-A have potential to increase wheat yields in breeding programs.

plant biology↗