Category Archives: ORIGINAL ARTICLE

Common signatures of selection reveal target loci for breeding across soybean populations

Posted on 23 January 2024 by

Abstract

Understanding the underlying genetic bases of yield-related selection and distinguishing these changes from genetic drift are critical for both improved understanding and future success of plant breeding. Soybean [Glycine max (L.) Merr.] is a key species for world food security, yet knowledge of the mechanism of selective breeding in soybean, such as the century-long program of artificial selection in U.S. soybean germplasm, is currently limited to certain genes and loci. Here, we identify genome-wide signatures of selection in separate populations of soybean subjected to artificial selection for increased yield by multiple breeding programs in the United States. We compared the alternative soybean breeding population (AGP) created by USDA-ARS to the conventional public soybean lines (CGP) developed at three different stages of breeding (ancestral, intermediate, and elite) to identify shared signatures of selection and differentiate these from drift. The results showed a strong selection for specific haplotypes identified by single site frequency and haplotype homozygosity methods. A set of common selection signatures was identified in both AGP and CGP that supports the hypothesis that separate breeding programs within similar environments coalesce on the fixation of the same key haplotypes. Signatures unique to each breeding program were observed. These results raise the possibility that selection analysis can allow the identification of favorable alleles to enhance directed breeding approaches.

Identification of haplotypes associated with resistance to Fusarium graminearum in spring oat (Avena sativa L.)

Posted on 23 January 2024 by

Abstract

Fusarium head blight (FHB) is the predominant disease in oat in Norway caused by the fungus Fusarium graminearum. It causes yield loss, reduced seed quality, reduced germination ability and accumulation of deoxynivalenol (DON). The FHB resistance is quantitative, and most genes have small effect. Markers with verified effect in the breeding program could further enhance the resistance breeding. This study aims to use a large and diverse population of 541 lines to identify quantitative trait loci (QTL) associated to FHB resistance in a genome-wide association study (GWAS) and verify their effect in independent breeding material. The material has been tested in six environments over three years and two locations in spawn inoculated and mist irrigated disease trials. The traits tested were germination ability and DON accumulation. A total of 15 significant QTL-regions were detected across 12 different linkage groups. Haplotypes for each region was constructed and the effect of the alleles in each environment was calculated, which identified the most likely resistant and susceptible alleles. Five QTL-regions were validated showing consistent effect in the GWAS population and the breeding material. Stacking of the resistant alleles of these regions from zero to five showed significant decrease in DON values and increased germination ability. The haplotype information of a set of historical and modern Nordic varieties were analysed, and the results could be used to select parents for future crossings. The validated haplotypes from this study can be used either to do marker assisted selection (MAS) or improve genomic prediction models in breeding programs.

Volatile organic compounds as potential biomarkers of Cadophora luteo‐olivacea presence on kiwifruits

Posted on 22 January 2024 by

The results suggested that the volatile compounds are released during the early phase of the interaction between kiwifruit (host) and Cadophora luteo-olivacea (pathogen).

Abstract

Cadophora luteo-olivacea is the causal agent of the skin-pitting disease of kiwifruit, a syndrome that appears after 4–5 months of cold storage. However, it is assumed that the infection takes place in the field during fruit development. The present work takes into consideration the production of volatile organic compounds (VOCs) of Actinidia deliciosa ‘Hayward’ at different phenological phases as potential C. luteo-olivacea infection biomarkers. In vitro assays were conducted to gain knowledge on the effect of kiwifruit VOCs on pathogen conidial germination and mycelial growth. VOCs produced by kiwifruit either inoculated or not with C. luteo-olivacea were analysed at different phenological phases by SPME/GC–MS analysis. In particular, ethanol, o -xylene, d-limonene and acetic acid showed a significant increase in the presence of fungal inoculation. Ethanol and d-limonene were also detected as volatile metabolites of the pathogen. The effect of each compound (ethanol, o -xylene, d-limonene and acetic acid) was tested on the fungal conidial germination at different concentrations, showing a growth stimulation at lower amounts. These results show how the production of some VOCs can contribute to the knowledge of fruit–pathogen interaction in the field with the aim of developing future tools for early disease detection and consequent effective control.

Long‐ and short‐read sequencing methods discover distinct circular RNA pools in Lotus japonicus

Posted on 20 January 2024 by

Abstract

Circular RNAs (circRNAs) are covalently closed single-stranded RNAs, generated through a back-splicing process that links a downstream 5′ site to an upstream 3′ end. The only distinction in the sequence between circRNA and their linear cognate RNA is the back splice junction. Their low abundance and sequence similarity with their linear origin RNA have made the discovery and identification of circRNA challenging. We have identified almost 6000 novel circRNAs from Lotus japonicus leaf tissue using different enrichment, amplification, and sequencing methods as well as alternative bioinformatics pipelines. The different methodologies identified different pools of circRNA with little overlap. We validated circRNA identified by the different methods using reverse transcription polymerase chain reaction and characterized sequence variations using nanopore sequencing. We compared validated circRNA identified in L. japonicus to other plant species and showed conservation of high-confidence circRNA-expressing genes. This is the first identification of L. japonicus circRNA and provides a resource for further characterization of their function in gene regulation. CircRNAs identified in this study originated from genes involved in all biological functions of eukaryotic cells. The comparison of methodologies and technologies to sequence, identify, analyze, and validate circRNA from plant tissues will enable further research to characterize the function and biogenesis of circRNA in L. japonicus.

Genome‐wide SNP discovery and genotyping delineates potential QTLs underlying major yield‐attributing traits in buckwheat

Posted on 18 January 2024 by

Abstract

Buckwheat (Fagopyrum spp.) is an important nutritional and nutraceutical-rich pseudo-cereal crop. Despite its obvious potential as a functional food, buckwheat has not been fully harnessed due to its low yield, self-incompatibility, increased seed cracking, limited seed set, lodging, and frost susceptibility. The inadequate availability of genomics resources in buckwheat is one of the major reasons for this. In the present study, genome-wide association mapping (GWAS) was conducted to identify loci associated with various morphological and yield-related traits in buckwheat. High throughput genotyping by sequencing led to the identification of 34,978 single nucleotide polymorphisms that were distributed across eight chromosomes. Population structure analysis grouped the genotypes into three sub-populations. The genotypes were also characterized for various qualitative and quantitative traits at two diverse locations, the analysis of which revealed a significant difference in the mean values. The association analysis revealed a total of 71 significant marker–trait associations across eight chromosomes. The candidate genes were identified near 100 Kb of quantitative trait loci (QTLs), providing insights into several metabolic and biosynthetic pathways. The integration of phenology and GWAS in the present study is useful to uncover the consistent genomic regions, related markers associated with various yield-related traits, and potential candidate genes having implications for being utilized in molecular breeding for the improvement of economically important traits in buckwheat. Moreover, the identified QTLs will assist in tracking the desirable alleles of target genes within the buckwheat breeding populations/germplasm.

Modelling the displacement and coexistence of clonal lineages of Phytophthora infestans through revisiting past outbreaks

Posted on 18 January 2024 by nChih‐Chiang Huang, nEdward C. Y. Liew, nJustin S. H. Wann

A simulation model with pathogenesis parameters as inputs was developed to predict the changes in lineage proportions of Phytophthora infestans on potato and tomato crops.

Abstract

The continuous changes in the lineage proportions of populations in the clonal plant pathogen Phytophthora infestans on potato and tomato crops have been perplexing to researchers and disease managers. Sudden outbreaks of newly emergent genotypes are often associated with these rapid composition changes. Modelling can predict the persistence and displacement of pathogen genotypes with differential fitness among hosts. Building upon previous models, we combined analytical and simulation methods to model the outcome of interactions between competing lineages on different hosts. Model inputs include pathogenesis parameters, and the outputs are fitness and lineage proportions within each host. Analytical solutions yielding complete displacement, partial coexistence-displacement and complete coexistence were described. In a retrospective study, the lesion growth rate and sporulation density of P. infestans lineages on potato and tomato from pathogenicity trials were used as inputs. Output lineage frequencies were compared with historical epidemiological situations to check model accuracy. The results showed that pathogenesis traits measured from empirical trials could simulate lineage constituents on potato and tomato and estimate genotypic fitness with reasonable accuracy. The model also showed promise in predicting ongoing lineage displacements in the subsequent year or few years, even when the displaced lineage was still highly prevalent during the time of isolation. However, large uncertainties remain at temporal–spatial scales owing to complex meta-population dynamics in some regions and adaptation to local environmental factors. This simulation model provides a new tool for forecasting pathogen compositions and can be used to identify potentially problematic genotypes based on pathogen life-history traits.

Genome‐wide development of intra‐ and inter‐specific transferable SSR markers and construction of a dynamic web resource for yam molecular breeding: Y2MD

Posted on 17 January 2024 by

Abstract

Microsatellite markers are widely used in population genetics and breeding. Despite the economic significance of yams in developing countries, there is a paucity of microsatellite markers, and as of now, no comprehensive microsatellite marker database exists. In this study, we conducted genome-wide microsatellite marker development across four yam species, identified cross-species transferable markers, and designed an easy-to-use web portal for the yam researchers. The screening of Dioscorea alata, Dioscorea rotundata, Dioscorea dumetorum, and Dioscorea zingiberensis genomes resulted in 318,713, 322,501, 307,040, and 253,856 microsatellites, respectively. Mono-, di-, and tri-nucleotides were the most important types of repeats in the different species, and a total of 864,128 primer pairs were designed. Furthermore, we identified 1170 cross-species transferable microsatellite markers. Among them, 17 out of 18 randomly selected were experimentally validated with good discriminatory power, regardless of the species and ploidy levels. Ultimately, we created and deployed a dynamic Yam Microsatellite Markers Database (Y2MD) available at https://y2md.ucad.sn/. Y2MD is embedded with various useful tools such as JBrowse, Blast, insilicoPCR, and SSR Finder to facilitate the exploitation of microsatellite markers in yams. This study represents the first comprehensive microsatellite marker mining across several yam species and will contribute to advancing yam genetic research and marker-assisted breeding. The released user-friendly database constitutes a valuable platform for yam researchers.

First insights into the quantitative genetic composition of the female seed yield for an efficient hybrid seed production in wheat (Triticum aestivum L.)

Posted on 16 January 2024 by

Abstract

Hybrid breeding of wheat (Triticum aestivum L.) is limited by its self-pollinating nature. Past cross-pollination improvements mostly focused on optimizing male traits. We tested the hybrid seed yield of 100 diverse elite lines treated with a chemical hybridization agent (CHA) and pollinated by non-sterilized male plants in multi-environmental field trials. Plant height and phenological traits of female plants were also assessed. In parallel, control experiments without CHA sterilization were conducted to measure per se yield of the tested material. Hybrid seed yield variation is of quantitative genetic nature, and, despite the large environmental influence, this trait has a strong genotypic component and is highly heritable (h ² = .77). The lack of correlation between hybrid seed yield and per se yield suggests a non-shared genetic control. Phenological traits and their interactions are important factors explaining together ~1/3 of hybrid seed yield variation. In contrast to plant height and flowering traits, which are influenced by major genetic factors, no significant marker–trait associations were found for the hybrid seed yield, thus suggesting a highly polygenic genetic architecture and the need of larger populations to investigate female hybrid seed yield.

Control of crown rot with potassium carbonate in banana cv. Enano Gigante

Posted on 15 January 2024 by

Incidence of banana postharvest crown rot caused by artificial infection with Colletotrichum musae can be reduced by 91.6% with treatments of potassium carbonate, a ‘generally recognized as safe’ (GRAS) substance, at 175 mM.

Abstract

The postharvest antifungal activity of potassium carbonate (PC) against crown rot (CR) was investigated in banana cv. Enano Gigante by artificially inoculating with Colletotrichum musae (Cm) and incubating at 25 ± 1°C for 7 days. PC treatments were tested by in vitro and in vivo primary experiments. The in vivo preliminary concentration of 175 mM PC was selected as the most effective and was used in subsequent experiments on the influence of dip temperature on the effectiveness of PC. Curative dip treatments of 175 mM PC at 40°C for 20 min applied alone or combined with low doses of thiabendazole (TBZ) were evaluated on CR. Finally, the effect of PC on banana fruit quality was determined. PC at 150 and 200 mM totally inhibited mycelial growth and conidial germination of Cm. In in vivo primary experiments, 175 mM PC significantly reduced both the incidence (33.3% reduction) and the severity (90.5% reduction) of CR, but only in curative treatments. When the 175 mM PC dip for 20 min was tested at different temperatures, the curative dip at 40°C was the most effective, reducing CR incidence and severity by 91.6% and 98.8%, respectively, and was used for subsequent experiments. PC combined with TBZ at 225 μL L⁻¹ did not improve the curative control effectiveness on CR compared to PC alone. PC did not affect the quality of banana fruit.

Genome‐wide association mapping for field spot blotch resistance in South Asian spring wheat genotypes

Posted on 14 January 2024 by

Abstract

Spot blotch caused by Bipolaris sorokiniana ((Sacc.) Shoemaker) (teleomorph: Cochliobolus sativus [Ito and Kuribayashi] Drechsler ex Dastur) is an economically important disease of warm and humid regions. The present study focused on identifying resistant genotypes and single-nucleotide polymorphism (SNP) markers associated with spot blotch resistance in a panel of 174 bread spring wheat lines using field screening and genome-wide association mapping strategies. Field experiments were conducted in Agua Fria, Mexico, during the 2019–2020 and 2020–2021 cropping seasons. A wide range of phenotypic variation was observed among genotypes tested during both years. Twenty SNP markers showed significant association with spot blotch resistance on 15 chromosomes, namely, 1A, 1B, 2A, 2B, 2D, 3A, 3B, 4B, 4D, 5A, 5B, 6A, 6B, 7A, and 7B. Of these, two consistently significant SNPs on 5A, TA003225-0566 and TA003225-1427, may represent a new resistance quantitative trait loci. Further, in the proximity of Tsn1 on 5B, AX-94435238 was the most stable and consistent in both years. The identified genomic regions could be deployed to develop spot blotch-resistant genotypes, particularly in the spot blotch-vulnerable wheat growing areas.