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Differential aggressiveness of Austropuccinia psidii isolates from guava and rose apple upon cross‐inoculation

Posted on 15 December 2023 by

Austropuccinia psidii isolates from guava and rose apple showed high pathogenic specialization to their original hosts and were unable to sporulate in heterospecific host–pathogen combinations.

Abstract

Myrtle rust, caused by Austropuccinia psidii, has been associated with more than 480 plant species belonging to the family Myrtaceae. Intraspecific variability in pathogenicity has been reported among isolates of A. psidii from different hosts. However, there are few studies that have comparatively quantified the disease in guava (Psidium guajava) and rose apple (Syzygium jambos). The objective of this work was to quantify the pathogenic variability of A. psidii isolates collected from guava and rose apple in Brazil and to investigate the mechanisms of infection and colonization of the pathogen at the cellular level. The monocyclic components of the rust disease were evaluated on young leaves of rose apple and guava plants cross-inoculated with isolates from rose apple and guava. Pathogenic specialization of both A. psidii isolates for their respective hosts was confirmed in this work. The guava A. psidii isolate was able to infect and colonize rose apple leaf tissues but no sporulation occurred. Similarly, the rose apple A. psidii isolate infected guava plants but did not sporulate. Confocal laser scanning microscopy revealed that lobed haustoria were present within rose apple leaves at 2 days post-inoculation (dpi) with both isolates, which resulted in intense mesophyll colonization for both interactions at 9 dpi. The latter is remarkable because infection of rose apple with the guava A. psidii isolate did not result in mature rust pustules.

The genetic architecture of the adaptive potential of Arabidopsis thaliana in response to Pseudomonas syringae strains isolated from south‐west France

Posted on 15 December 2023 by

By conducting a GWAS on an ecologically relevant pathosystem, we identified a polygenic architecture underlying the adaptive potential of the response of Arabidopsis thaliana to a non-native Pseudomonas syringae pathogenic strain.

Abstract

Phytopathogens are a threat for global food production and security. Emergence or re-emergence of plant pathogens is highly dependent on the environmental conditions affecting pathogen spread and survival. Under climate change, a geographic expansion of pathogen distribution poleward has been observed, potentially resulting in disease outbreaks on crops and wild plants. Therefore, estimating the adaptive potential of plants to novel epidemics and describing the underlying genetic architecture is a primary need to propose agricultural management strategies reducing pathogen outbreaks and to breed novel plant cultivars adapted to pathogens that might spread under climate change. To address this challenge, we inoculated Pseudomonas syringae strains isolated from Arabidopsis thaliana populations from south-west of France on the highly genetically polymorphic TOU-A A. thaliana population from north-east France. While no adaptive potential was identified in response to most P. syringae strains, the TOU-A population displayed a variable disease response to the JACO-CL strain belonging to the P. syringae phylogroup 7 (PG7). This strain carried a reduced type III secretion system (T3SS) characteristic of the PG7 as well as flexible genomic traits and potential novel effectors. Genome-wide association mapping on 192 TOU-A accessions revealed a polygenic architecture of disease response to JACO-CL. The main quantitative trait locus (QTL) region encompasses two R genes and the AT5G18310 gene encoding ubiquitin hydrolase, a target of the AvrRpt2 P. syringae effector. Altogether, our results pave the way for a better understanding of the genetic and molecular basis of the adaptive potential in an ecologically relevant A. thaliana–P. syringae pathosystem.

Identification of a new Rsg1 allele conferring resistance to multiple greenbug biotypes from barley accessions PI 499276 and PI 566459

Posted on 13 December 2023 by

Abstract

Greenbug [Schizaphis graminum (Rondani)] is a major insect pest that significantly affects barley production worldwide. The identification of novel greenbug resistance genes is crucial for sustainable barley production and global food security. To identify greenbug resistance genes from a US breeding line PI 499276 and a Chinese cultivar PI 566459, two F_6:7 recombinant inbred line (RIL) populations developed from crosses Weskan × PI 499276 and Weskan × PI 566459 were phenotyped for responses to greenbug biotype E and genotyped using genotyping-by-sequencing (GBS). Linkage analysis using single nucleotide polymorphism and kompetitive allele-specific polymorphism (KASP) markers delimited the greenbug resistance genes from PI 499276 and PI 566459 to a 1.2 Mb genomic region between 666.5 and 667.7 Mb on the long arm of chromosome 3H in the Morex Hordeum vulgare r1 reference sequence. Allelism tests based on responses of four F₂ populations to greenbug biotype E indicated that the greenbug resistance gene in PI 499276 and PI 566459 is either allelic or very close to Rsg1. Given that PI 499276 and PI 566459 shared the same unique resistance pattern to a set of 14 greenbug biotypes, which is different from those of other Rsg1 alleles, they carry a new Rsg1 allele. The greenbug resistance genes in Post 90, PI 499276/PI 566459, and WBDC 336 were designated as Rsg1.a1, Rsg1.a2, and Rsg1.a3, respectively. KASP markers KASP-Rsg1a3-1, KASP-Rsg1a3-2, and KASP160 can be used to tag Rsg1.a2 in barley breeding.

Identification of diagnostic KASP‐SNP markers for routine breeding activities in yam (Dioscorea spp.)

Posted on 13 December 2023 by

Abstract

Maintaining genetic purity and true-to-type clone identification are important action steps in breeding programs. This study aimed to develop a universal set of kompetitive allele-specific polymerase chain reaction (KASP)-based single nucleotide polymorphism (SNP) markers for routine breeding activities. Ultra-low-density SNP markers were created using an initial set of 173,675 SNPs that were obtained from whole-genome resequencing of 333 diverse white Guinea yam (Dioscorea rotundata Poir) genotypes. From whole-genome resequencing data, 99 putative SNP markers were found and successfully converted to high-throughput KASP genotyping assays. The markers set was validated on 374 genotypes representing six yam species. Out of the 99 markers, 50 were highly polymorphic across the species and could distinguish different yam species and pedigree origins. The selected SNP markers classified the validation population based on the different yam species and identified potential duplicates within yam species. Through penalized analysis, the male parent of progenies involved in polycrosses was successfully predicted and validated. Our research was a trailblazer in validating KASP-based SNP assays for species identification, parental fingerprinting, and quality control (QC) and quality assurance (QA) in yam breeding programs.

A new wild emmer wheat panel allows to map new loci associated with resistance to stem rust at seedling stage

Posted on 12 December 2023 by

Abstract

Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is a major wheat disease worldwide. A collection of 283 wild emmer wheat [Triticum turgidum L. subsp. dicoccoides (Körn. ex Asch. & Graebn.) Thell] accessions, representative of the entire Fertile Crescent region where wild emmer naturally occurs, was assembled, genotyped, and characterized for population structure, genetic diversity, and rate of linkage disequilibrium (LD) decay. Then, the collection was employed for mapping Pgt resistance genes, as a proof of concept of the effectiveness of genome-wide association studies in wild emmer. The collection was evaluated in controlled conditions for reaction to six common Pgt pathotypes (TPMKC, TTTTF, JRCQC, TRTTF, TTKSK/Ug99, and TKTTF). Most resistant accessions originated from the Southern Levant wild emmer lineage, with some showing a resistance reaction toward three to six tested races. Association analysis was conducted considering a 12K polymorphic single-nucleotide polymorphisms dataset, kinship relatedness between accessions, and population structure. Eleven significant marker–trait associations (MTA) were identified across the genome, which explained from 17% to up to 49% of phenotypic variance with an average 1.5 additive effect (based on the 1–9 scoring scale). The identified loci were either effective against single or multiple races. Some MTAs colocalized with known Pgt resistance genes, while others represent novel resistance loci useful for durum and bread wheat prebreeding. Candidate genes with an annotated function related to plant response to pathogens were identified at the regions linked to the resistance and defined according to the estimated small LD (about 126 kb), as typical of wild species.

Selection for drought tolerance in backcross populations derived from interspecific crosses of Solanum lycopersicum × Solanum pennellii

Posted on 11 December 2023 by

Abstract

Drought strongly limits tomato yield, and the introgression of genes from wild tomatoes is a powerful tool to obtain drought-tolerant progenies. The aim of this study was to select drought-tolerant transgressive progeny obtained from interspecific crosses between drought-susceptible tomatoes (Solanum lycopersicum) × drought-tolerant wild species (Solanum pennellii) under in vitro and greenhouse conditions. BC₁F₂ populations were advanced from backcrosses between F₁ × Jumbo AG-592 (cultivar for fresh consumption) and F₁ × BRS Tospodoro (cultivar for industrial processing). For this, BC₁F₂ seeds were germinated in vitro and evaluated for tolerance to drought. Then, eight genotypes from each BC₁F₂ were selected and submitted to 14 days of drought (0% of water supply) or well-watered (100% of water supply) in greenhouse conditions and evaluated for growth, water balance and gas exchanges. Using in vitro assays with mannitol-induced drought proved to be effective for the initial screening of drought-tolerant BC₁F₂ plants, while greenhouse experiments showed that drought decreased photosynthesis in all genotypes, but almost all the BC₁F₂ progenies had greater photosynthetic capacity, water balance and growth than their commercial parents. As a result, we selected six progenies for fresh consumption and six progenies for industrial processing with increased drought tolerance.

Use of continuous genotypes for genomic prediction in sugarcane

Posted on 8 December 2023 by

Abstract

Genomic selection in sugarcane faces challenges due to limited genomic tools and high genomic complexity, particularly because of its high and variable ploidy. The classification of genotypes for single nucleotide polymorphisms (SNPs) becomes difficult due to the wide range of possible allele dosages. Previous genomic studies in sugarcane used pseudo-diploid genotyping, grouping all heterozygotes into a single class. In this study, we investigate the use of continuous genotypes as a proxy for allele-dosage in genomic prediction models. The hypothesis is that continuous genotypes could better reflect allele dosage at SNPs linked to mutations affecting target traits, resulting in phenotypic variation. The dataset included genotypes of 1318 clones at 58K SNP markers, with about 26K markers filtered using standard quality controls. Predictions for tonnes of cane per hectare (TCH), commercial cane sugar (CCS), and fiber content (Fiber) were made using parametric, non-parametric, and Bayesian methods. Continuous genotypes increased accuracy by 5%–7% for CCS and Fiber. The pseudo-diploid parametrization performed better for TCH. Reproducing kernel Hilbert spaces model with Gaussian kernel and AK4 (arc-cosine kernel with hidden layer 4) kernel outperformed other methods for TCH and CCS, suggesting that non-additive effects might influence these traits. The prevalence of low-dosage markers in the study may have limited the benefits of approximating allele-dosage information with continuous genotypes in genomic prediction models. Continuous genotypes simplify genomic prediction in polyploid crops, allowing additional markers to be used without adhering to pseudo-diploid inheritance. The approach can particularly benefit high ploidy species or emerging crops with unknown ploidy.

Durum wheat heat tolerance loci defined via a north–south gradient

Posted on 7 December 2023 by

Abstract

The global production of durum wheat (Triticum durum Desf.) is hindered by a constant rise in the frequency of severe heat stress events. To identify heat-tolerant germplasm, three different germplasm panels (“discovery,” “investigation,” and “validation”) were studied under a range of heat-stressed conditions. Grain yield (GY) and its components were recorded at each site and a heat stress susceptibility index was calculated, confirming that each 1°C temperature rise corresponds to a GY reduction in durum wheat of 4.6%–6.3%. A total of 2552 polymorphic single nucleotide polymorphisms (SNPs) defined the diversity of the first panel, while 5642 SNPs were polymorphic in the “investigation panel.” The use of genome-wide association studies revealed that 36 quantitative trait loci were associated with the target traits in the discovery panel, of which five were confirmed in a “subset” tested imposing heat stress by plastic tunnels, and in the investigation panel. A study of allelic combinations confirmed that Q.icd.Heat.003-1A, Q.icd.Heat.007-1B, and Q.icd.Heat.016-3B are additive in nature and the positive alleles at all three loci resulted in a 16% higher GY under heat stress. The underlying SNPs were converted into kompetitive allele specific PCR markers and tested on the validation panel, confirming that each explained up to 9% of the phenotypic variation for GY under heat stress. These markers can now be used for breeding to improve resilience to climate change and increase productivity in heat-stressed areas.

Characterization of temperate and tropical popcorn populations and GWAS for zeins and starch contents

Posted on 4 December 2023 by

Abstract

Because measuring expansion volume (EV) is simple and inexpensive, popcorn breeders have developed high-quality single crosses ignoring the contents of zeins, starch, lipids, and cellular wall components in selection. However, some methods of quantification of these quality-related traits can be applied to popcorn breeding, increasing the selection efficacy for quality. The objectives of this study were to assess methods of zeins and starch quantification that can be used in popcorn breeding, characterize a temperate and a tropical populations for zeins and starch contents and identify candidate genes for these quality-related traits. We genotyped and phenotyped 286 plants. For quantification of total zeins and zein subunits we choose the ‘lab-on-a-chip’ microfluidic electrophoresis. For quantification of starch and amylose/amylopectin, we choose the Megazyme's Amylose/Amylopectin kit assay. The temperate population has superior EV (36.0%), a higher level of the 19 kDa zein subunit (32.0%), lower levels of the 21, 22 and 27 kDa subunits (−1543.0%, −40.0% and −47.0%, respectively) and no statistical difference for the 10 kDa zein content, relative to the tropical population. Although there are statistical differences between the two populations regarding starch, amylose, and amylose/amylopectin ratio, the differences are not significant (−2.0% to 8.0%). Thirteen candidate genes were identified for the 19 and 22 kDa zeins, two for amylose and one for starch, with emphasis on the genes coding for the 19 and 22 kDa alpha-zeins, located on chromosome 4. The evaluated quantification methods can be used in popcorn breeding but for a limited number of samples, mainly because costs.

Overexpression of the TaEXPA19 gene improves low‐temperature tolerance in winter wheat (Triticum aestivum)

Posted on 28 November 2023 by

Abstract

Low temperature is one of the main abiotic stresses that affects plant growth, causing serious damage or even death to plants. The differential expression of the TaEXPA19 gene in the above and underground parts of winter wheat and the implications for cold resistance remain unclear. In this study, the TaEXPA19 gene was cloned and analysed for expression in winter wheat, and transgenic Arabidopsis thaliana was constructed to investigate the effect of the TaEXPA19 gene in response to low-temperature stress on plant growth. The TaEXPA19-A and TaEXPA19-D genes have different response patterns in the above and underground parts of transgenic A. thaliana. When plants were subjected to low-temperature stress, the leaves were quickly upregulated and the roots were downregulated, and then upregulated to respond to low-temperature stress to promote the growth of leaf length and leaf width petiole length. The results indicated that TaEXPA19 genes could improve low-temperature tolerance in plants. The results of this study laid a foundation for the study of the cold resistance of winter wheat.