Category Archives: ORIGINAL ARTICLE

Genomic selection of soybean (Glycine max) for genetic improvement of yield and seed composition in a breeding context

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Abstract

Genomic selection has been utilized for genetic improvement in both plant and animal breeding and is a favorable technique for quantitative trait development. Within this study, genomic selection was evaluated within a breeding program, using novel validation methods in addition to plant materials and data from a commercial soybean (Glycine max) breeding program. A total of 1501 inbred lines were used to test multiple genomic selection models for multiple traits. Validation included cross-validation, inter-environment, and empirical validation. The results indicated that the extended genomic best linear unbiased prediction (EGBLUP) model was the most effective model tested for yield, protein, and oil in cross-validation with accuracies of 0.50, 0.68, and 0.64, respectively. Increasing marker number from 1000 to 3000 to 6000 single nucleotide polymorphism markers leads to statistically significant increases in accuracy. Cross-environment predictions were statistically lower than cross-validation with accuracies of 0.24, 0.54, and 0.42 for yield, protein, and oil, respectively, using the extended genomic BLUP model. Empirical validation, predicting the yield of 510 soybean lines, had a prediction accuracy of 0.34, with the inclusion of a maturity covariate leading to a notable increase in accuracy. Genomic selection identified high-performance lines in inter-environment predictions: 34% of lines within the upper quartile of yield, and 51% and 48% of the highest quartile protein and oil lines, respectively. Statistically similar results occurred comparing rankings in empirical validation and selection for advancements in yield trials. These results indicate that genomic selection is a useful tool for selection decisions.

A new set of international Leptosphaeria maculans isolates as a resource for elucidation of the basis and evolution of blackleg disease on Brassica napus

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A new set of international Leptosphaeria maculans isolates as a resource for elucidation of the basis and evolution of blackleg disease on Brassica napus

An international collection of Leptosphaeria maculans isolates has been established as a key resource to help understand the interaction between this fungal pathogen and its host, canola (Brassica napus).


Abstract

A collection of isolates of the fungi Leptosphaeria maculans and L. biglobosa, which cause blackleg disease on Brassica napus (canola/oilseed rape) and other Brassicaceae species, was assembled to represent the global diversity of these pathogens and a resource for international research. The collection consists of 226 isolates (205 L. maculans and 21 L. biglobosa) from 11 countries. The genomes of all 205 L. maculans isolates were sequenced, and the distribution and identity of avirulence gene alleles were determined based on genotypic information and phenotypic reactions on B. napus lines that hosted specific resistance genes. Whilst the frequencies of some avirulence alleles were consistent across each of the regions, others differed dramatically, potentially reflecting the canola/oilseed rape cultivars grown in those countries. Analyses of the single-nucleotide polymorphism (SNP) diversity within these L. maculans isolates revealed geographical separation of the populations. This "open access" resource provides a standardized set of isolates that can be used to define the basis for how these fungal pathogens cause disease, and as a tool for discovery of new resistance traits in Brassica species.

Combinatory ability and heterosis for quantitative traits related to productivity and the pungency in F1 hybrids of habanero pepper (Capsicum chinense Jacq.)

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Abstract

The objective of this work was to obtain high-yielding F1 hybrids of the habanero pepper, using 10 outstanding parents in a line-tester genetic design. General combinatorial ability and specific combinatorial ability were evaluated in the parents' and the hybrids F1 obtained, respectively. Heterosis was determined in the 18 hybrids obtained. The technique of HPLC was used to evaluate the capsaicin content in the fruit of 10 parents and 18 hybrids of habanero pepper. The DNA profiles were analysed as part of the characterization of the germplasm of the species conserved at the CICY. Furthermore, the molecular variation of the genotypes under investigation was assessed using eight SSR and nine ISSR markers. The results showed the presence of substantial morphoagronomic and molecular variability among the habanero pepper genotypes evaluated. Genetic similarities of 83%–93% between parents and 76%–94% between hybrids were found. The most productive hybrids were H8, H10 and H19 with 3.13 to 4.29 kg/plant, respectively, these came from crosses where RNJ-04 (P26) as the male parent and the hybrid H60 (4.92 kg/plant) that comes from the male parent RES-08 (P30). Likewise, the H7 hybrid had the highest capsaicin content (128.41 mg/g dry weight, 960,687.00 SHU). Hybrids H43 with 114.39 mg/g DW and 90,444.30 SHU, and H51 with 11.61 mg/g DW and 934,745.07 SHU respectively, also stood out.

Genomic prediction with machine learning in sugarcane, a complex highly polyploid clonally propagated crop with substantial non‐additive variation for key traits

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Abstract

Sugarcane has a complex, highly polyploid genome with multi-species ancestry. Additive models for genomic prediction of clonal performance might not capture interactions between genes and alleles from different ploidies and ancestral species. As such, genomic prediction in sugarcane presents an interesting case for machine learning (ML) methods, which are purportedly able to deal with high levels of complexity in prediction. Here, we investigated deep learning (DL) neural networks, including multilayer networks (MLP) and convolution neural networks (CNN), and an ensemble machine learning approach, random forest (RF), for genomic prediction in sugarcane. The data set used was 2912 sugarcane clones, scored for 26,086 genome wide single nucleotide polymorphism markers, with final assessment trial data for total cane harvested (TCH), commercial cane sugar (CCS), and fiber content (Fiber). The clones in the latest trial (2017) were used as a validation set. We compared prediction accuracy of these methods to genomic best linear unbiased prediction (GBLUP) extended to include dominance and epistatic effects. The prediction accuracies from GBLUP models were up to 0.37 for TCH, 0.43 for CCS, and 0.48 for Fiber, while the optimized ML models had prediction accuracies of 0.35 for TCH, 0.38 for CCS, and 0.48 for Fiber. Both RF and DL neural network models have comparable predictive ability with the additive GBLUP model but are less accurate than the extended GBLUP model.

Genetic erosion within the Fabada dry bean market class revealed by high‐throughput genotyping

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Abstract

The Fabada market class within the dry beans has a well-differentiated seed phenotype with very large white seeds. This work investigated the genetic diversity maintained in the seed collections within this market class and possible genetic erosion over the last 30 years. A panel with 100 accessions was maintained in seed collections for 30 years, 57 accessions collected from farmers in 2021, six cultivars developed in SERIDA, and 16 reference cultivars were gathered and genotyped with 108,585 SNPs using the genotyping-by-sequencing method. Filtering based on genotypic and phenotypic data was carried out in a staggered way to investigate the genetic diversity among populations. The dendrogram generated from genotyping revealed 90 lines forming 16 groups with identical SNP profiles (redundant lines) from 159 lines classified as market-class Fabada according to their passport data. Seed phenotyping indicated that 19 lines were mistakenly classified as Fabada (homonymies), which was confirmed in the dendrogram built without redundant lines. Moreover, this study provides evidence of genetic erosion between the population preserved for 30 years and the currently cultivated population. The conserved population contains 54.6% segregation sites and 41 different SNP profiles, whereas the cultivated population has 19.6% segregation sites and 26 SNP profiles. The loss of genetic variability cannot be attributed to the diffusion of modern cultivars, which increase genetic diversity (six new SNP profiles). The results allow for the more efficient preservation of plant genetic resources in genebanks, minimizing redundant accessions and incorporating new variations based on genotypic and phenotypic data.

Genome‐wide association study of soluble solids content, flesh color, and fruit shape in citron watermelon

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Abstract

Fruit quality traits are crucial determinants of consumers’ willingness to purchase watermelon produce, making them major goals for breeding programs. There is limited information on the genetic underpinnings of fruit quality traits in watermelon. A total of 125 citron watermelon (Citrullus amarus) accessions were genotyped using single nucleotide polymorphisms (SNPs) molecular markers generated via whole-genome resequencing. A total of 2,126,759 genome-wide SNP markers were used to uncover marker-trait associations using single and multi-locus GWAS models. High broad-sense heritability for fruit quality traits was detected. Correlation analysis among traits revealed positive relationships, with the exception of fruit diameter and fruit shape index (ratio of fruit length to fruit diameter), which was negative. A total of 37 significant SNP markers associated with soluble solids content, flesh color, fruit length, fruit diameter, and fruit shape index traits were uncovered. These peak SNPs accounted for 2.1%–23.4% of the phenotypic variation explained showing the quantitative inheritance nature of the evaluated traits. Candidate genes relevant to fruit quality traits were uncovered on chromosomes Ca01, Ca03, Ca06, and Ca07. These significant molecular markers and candidate genes will be useful in marker-assisted breeding of fruit quality traits in watermelon.

Morphological and pathological characterization of Colletotrichum species causing anthracnose of litchi leaves in Guangxi, China

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Abstract

Litchi (Litchi chinensis Sonn.) is an evergreen subtropical fruit tree native to southern China. Litchi is vulnerable to a wide range of diseases affecting yield and fruit quality. Anthracnose is one of the main diseases during the period of growth and storage, which has a serious impact on the quality and production of litchi. In December 2020 to May 2021, typical anthracnose symptoms were observed on litchi leaves in different orchards in Qinzhou City, Guangxi Province, Southern China. According to colony features, conidial and appressorial morphology, and sequence analysis of several genomic regions (internal transcribed spacer (ITS) region, chitin synthase (chs-1), actin (act), calmodulin (cal), glyceraldehyde-3-phosphate dehydrogenase (gapdh), β-tubulin (tub2) and the intergenic region of apn2 and MAT1-2-1 (ApMat)), 44 isolates were obtained, and 26 were identified as three Colletotrichum species: C. fructicola (50%), C. siamense (42.31%), C. gigasporum (7.69%). The pathogenicity tests were performed with conidial suspension and mycelia plugs to inoculate wounded litchi seedlings. The results of pathogenicity tests showed that the virulence of C. gigasporum was the weakest, and the virulence of C. fructicola was the strongest. This is the first report of C. gigasporum causing anthracnose of litchi worldwide.

Characterization of causal agents of bacterial canker on apricot plantations and risk mapping using GIS in Aras Basin (Türkiye)

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Abstract

Bacterial canker of stone fruits caused by Pseudomonas syringae pv. syringae (Pss) and Pseudomonas syringae pv. morsprunorum (Psm race-1/Psm race-2) may lead to significant yield and crop losses in apricot (Prunus armeniaca L.) cultivation areas in Türkiye. Strains pathogenic to apricot were isolated from trees with symptoms (mainly necrotized buds and dieback) of bacterial canker in orchards in Aras Basin. Pathogens were characterized using pathogenicity tests, phenotypic assays, end-point PCR and multilocus sequence analysis (MLSA). Fifteen Pseudomonas syringae strains were isolated from 205 plant samples collected from apricot orchards showing symptoms of bacterial canker. As a consequence of the diagnostic tests, all isolates were identified as P. syringae pv. syringae. In this study, Pss, Psm R1 and Psm R2 strains in stone fruits were separated into different phylogroups (Pg-2, Pg-3, sPg-1b) based on MLSA. Turkish strains obtained from stone fruits, particularly apricot, showed genetic heterogeneity, and clustered in different sub-phylogroups (sPg-2b, sPg-2c, sPg-2d). All these strains except strain K258 are also clustered in the same sub-phylogroups (sPg-2b and sPg-2d) with other strains from different countries especially Iran, Lebanon, etc. Strain K258 isolated from apricot was clustered in sPg-2c with Pss strain 642 (USA). The risk of bacterial canker disease in apricot growing areas is considered using GIS in this study. It was determined that a significant part of the Iğdır Plain, the biggest agricultural area in the Aras Basin, is at very high risk.

The presence of the plant pathogen Fusarium graminearum as a soil inoculum enhances the rhizosphere survival of bacterial biocontrol strains aimed at the pathogen

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Abstract

The serious wheat pathogen Fusarium graminearum causes both root rot and head blight. Some classical biocontrol tests were first used to explore the biocontrol ability of 39 Pseudomonas fluorescens strains. The five most antifungal strains B4, P13, UTPf127, UTPf125 and UTPf105 were selected to screen known antifungal antibiotic genes and greenhouse experiments. The ability of bacteria to colonize wheat rhizosphere and their effect on plant growth in the presence and absence of soil F. graminearum inoculum was studied under greenhouse conditions. Overall, biocontrol bacteria populations were significantly higher in both wheat endo-and ectorhizosphere of pathogen-inoculated soil than in healthy soil. The population of all strains differently decreased with time. On day 28, endorhizosphere populations of strain B4 could be detected in inoculated but not healthy soil, while UTPf127 populations remained high in endorhizospheres at all tested times. Isolate B4 and UTPf105 showed the most substantial plant growth in pathogen-inoculated soil compared to pathogen-inoculated soil without added bacteria. UTPf127-treated plants grew better in control soil than when the pathogen was present. In contrast, UTPf125 and P13 showed little effect on plant growth. These results point to complex interactions between pathogen and biocontrol bacteria and suggest that a fungal pathogen in the soil can affect the survival of potential bacterial biological control agents. Additionally, they highlight the importance of screening and evaluating potential biocontrol bacteria against soilborne fungal pathogens by in vivo tests rather than relying on plate screenings.

Improper crop rotation may enrich soil‐borne pathogens of Panax notoginseng

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Abstract

Soil-borne diseases are the main cause of yield reduction of Panax notoginseng (Sanqi), and are mainly caused by the enrichment of pathogenic fungi during continuous cropping. In the Wenshan district of Yunnan province, China, where Sanqi is widely cultivated, the rotation of Foeniculum vulgare (fennel) crops with Sanqi crops is assumed to help reduce occurrences of rot in Sanqi roots. However, in a field investigation, we found that this practice actually increased incidences of root rot in Sanqi crops. Using fennel plants obtained from the cropping system, we tested the hypothesis that fennel crops enriched communities of pathogenic fungi of Sanqi. We isolated six endophytic fungi from the roots of fennel plants and identified these based on their morphological characteristics and a sequencing analysis. The isolates were identified as Fusarium oxysporum (FV-1-R-1, FV-2-R-1), Alternaria alternata (FV-3-R-1, FV-14-R-1), Pyricularia grisea (FV-8-R-1) and Colletotrichum truncatum (FV-11-R-4). In a series of inoculation experiments, we verified the pathogenicity of these fungi to Sanqi based on Koch's postulates, and demonstrated that all isolates caused root rot in Sanqi. Our results suggest that fennel is an inappropriate crop choice for rotation with Sanqi because it may serve as an intermediate host for the pathogenic fungi that cause root rot in Sanqi, and thereby exacerbate crop diseases. Our empirical findings provide useful information for enhancing the cultivation of Sanqi and the practice of crop rotation.