Category Archives: ORIGINAL ARTICLE

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

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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.

The alleles bc‐ud and bc‐ur (previously bc‐4 gene), representing coding mutations within Vps4 AAA+ ATPase ESCRT protein, interact with other genes to condition resistance to BCMV and BCMNV in common bean

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Abstract

Bean common mosaic virus (BCMV) and bean common mosaic necrosis virus (BCMNV) have a damaging impact on global common bean (Phaseolus vulgaris L.) cultivation, causing potential yield losses of over 80%. The primary strategy for controlling these viruses is through host plant resistance. This research aimed to identify and validate structural variations for the bc-u d gene as revealed by long-read sequencing, develop an efficient DNA marker to assist selection of bc-u d in snap and dry beans, and examine the interactions between the bc-u d allele and other BCMV resistance genes. A gene (Phvul.005G125100) model on chromosome Pv05, encoding a vacuolar protein-sorting 4 (Vps4) AAA+ ATPase endosomal sorting complexes required for transport (ESCRT) protein, was identified as the best candidate gene for bc-u d. An 84-bp repetitive insertion variant within the gene, exhibited 100% co-segregation with the bc-u d resistance allele across 264 common bean accessions. The 84-bp repetitive insertion was labeled with an indel marker IND_05_36225873 which was useful for tracking the bc-u d allele across diverse germplasm. A different single nucleotide polymorphism variant within the same candidate gene was associated with the bc-4 gene. Segregation in F2 populations confirmed bc-u d and bc-4 were alleles, so bc-4 was renamed bc-u r to fit gene nomenclature guidelines. The interactions of bc-u d and bc-u r with other resistance genes, such as bc-1 (receptor-like kinase on Pv03) and bc-2 (Vps4 AAA+ ATPase ESCRT protein on Pv11), validated gene combinations in the differential “host groups” effective against specific BCMV/BCMNV “pathogroups.” These findings increase our understanding of the Bc-u locus, and enhance our ability to develop more resilient bean varieties through marker-assisted selection, reducing the impact of BCMV and BCMNV.

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

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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

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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

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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.

Transcriptome analysis of iron over‐accumulating Arabidopsis genotypes uncover putative novel regulators of systemic and retrograde signaling

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Abstract

On account of its competence to accept and donate electrons, iron (Fe) is an essential element across all forms of life, including plants. Maintaining Fe homeostasis requires precise orchestration of its uptake, trafficking, and translocation in order to meet the demand for Fe sinks such as plastids. Plants harboring defects in the systemic Fe transporter OPT3 (OLIGOPEPTIDE TRANSPORTER 3) display constitutive Fe deficiency responses and accumulate toxic levels of Fe in their leaves. Similarly, ectopic expression of IRONMAN (IMA) genes, encoding a family of phloem-localized signaling peptides, triggers the uptake and accumulation of Fe by inhibiting the putative Fe sensor BRUTUS. This study aims at elucidating the mechanisms operating between OPT3-mediated systemic Fe transport, activation of IMA genes in the phloem, and activation of Fe uptake in the root epidermis. Transcriptional profiling of opt3-2 mutant and IMA1/IMA3 overexpressing (IMA Ox) lines uncovered a small subset of genes that were consistently differentially expressed across all three genotypes and Fe-deficient control plants, constituting potential novel regulators of cellular Fe homeostasis. In particular, expression of the the F-box protein At1g73120 was robustly induced in all genotypes, suggesting a putative function in the posttranslational regulation of cellular Fe homeostasis. As further constituents of this module, two plastid-encoded loci that putatively produce transfer ribonucleic acid (tRNA)-derived small ribonucleic acids are possibly involved in retrograde control of root Fe uptake.

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

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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)

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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.

Isolation of yellow vein mosaic virus (YVMV)‐resistant mutants of okra (Abelmoschus esculentus L.) through applied mutagenesis

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Okra, Abelmoschus esculentus (L.) Moench, being highly susceptible to yellow vein mosaic virus (YVMV) disease warrants its genetic improvement for resistance. Applied mutagenesis programme using two optimum doses of gamma radiation, namely, 350 Gy and 450 Gy radiation, was administered for the variety Pusa Sawani rated as excellent for fruit quality but highly susceptible to YVMV disease. Two selected putative mutant families, namely, 350//10///3-9////28 and 450//66///2-4////39, isolated in the M5 generation with slightly different plant morphology as compared to the parental genotype, Pusa Sawani, showed consistent resistance against YVMV disease. Upon evaluation in the M6 generation, eight morphological characteristics and five quantitative characteristics differed significantly among the mutants and Pusa Sawani. Proximate compositions and enzyme activity in leaf were significantly higher in the two YVMV-resistant mutants. Disease screening under artificial inoculation in the insect proof cages confirmed YVMV resistance in these mutants. DNA fingerprinting further validated the alterations occurred in these two isolated mutants compared to the parental genotype. These mutants deserve due attention towards the development of YVMV-resistant variety.

Genomic and phenotypic characterization of finger millet indicates a complex diversification history

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Advances in sequencing technologies mean that insights into crop diversification can now be explored in crops beyond major staples. We use a genome assembly of finger millet, an allotetraploid orphan crop, to analyze DArTseq single nucleotide polymorphisms (SNPs) at the whole and sub-genome level. A set of 8778 SNPs and 13 agronomic traits was used to characterize a diverse panel of 423 landraces from Africa and Asia. Through principal component analysis (PCA) and discriminant analysis of principal components, four distinct groups of accessions were identified that coincided with the primary geographic regions of finger millet cultivation. Notably, East Africa, presumed to be the crop's origin, exhibited the lowest genetic diversity. The PCA of phenotypic data also revealed geographic differentiation, albeit with differing relationships among geographic areas than indicated with genomic data. Further exploration of the sub-genomes A and B using neighbor-joining trees revealed distinct features that provide supporting evidence for the complex evolutionary history of finger millet. Although genome-wide association study found only a limited number of significant marker-trait associations, a clustering approach based on the distribution of marker effects obtained from a ridge regression genomic model was employed to investigate trait complexity. This analysis uncovered two distinct clusters. Overall, the findings suggest that finger millet has undergone complex and context-specific diversification, indicative of a lengthy domestication history. These analyses provide insights for the future development of finger millet.