Prof. Yuan Longping: The Father of Hybrid Rice revolutionized global agriculture by tremendously increasing rice production
Plant Breeding, Volume 143, Issue 1, Page 82-82, February 2024.
Special Issue on Breeding and breeding research for resistance to Fusarium diseases in cereals
Plant Breeding, Volume 143, Issue 1, Page 1-1, February 2024.
Issue Information
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Influence of berry ripening on susceptibility to Coniella diplodiella infection in grapevine
The data from in vitro and in vivo trials showed that grape clusters were susceptible to infection by Coniella diplodiella for a long period; effective disease control therefore requires interventions from early berry development.
Abstract
White rot, caused by the fungus Coniella diplodiella, is an important but poorly studied disease that mainly affects grapevine clusters. White rot control typically involves the repeated application of fungicides, which may be unjustified in some cases given that the key period of berry susceptibility to infection remains unclear and controversial. In this study, germination of C. diplodiella conidia and mycelium growth were investigated on water agar (conidial germination only) and artificial media similar to berry juice at five growth stages from pea-sized to berries ripe for harvest. On water agar, conidia germinated from 10°C to 35°C (with an optimum of 20–30°C) with >2 h of moisture incubation. Both conidial germination and mycelial growth were higher on agar similar to berry juice at véraison to berry softening than at other stages, with the lowest values detected for the ripe berries. The berries were also artificially inoculated with conidia at the different growth stages, showing that grape clusters were susceptible to infection for a long period, albeit with varying degrees of susceptibility at different stages. This implies that effective disease control requires interventions from early berry development, whenever weather conditions are conducive to infection. Further development of a predictive model accounting for weather conditions and berry susceptibility dynamics would facilitate the dynamic estimation of the disease risk during the grapevine-growing season and contribute to a risk-based application of fungicides for white rot control.
Differential expression of antimicrobial metabolites, phenylpropanoid and phytohormone metabolic pathway genes determines resistance or susceptibility to Ascochyta rabiei in chickpea
Defence to Ascochyta rabiei in chickpea is composed of a two-tier system separated by time wherein jasmonic acid, phenylpropanoids, antimicrobial peptides and defence genes govern resistance and abscisic acid susceptibility.
Abstract
Blight caused by Ascochyta rabiei is a major constraint in the productivity of chickpea (Cicer arietinum). The mechanisms governing resistance/susceptibility to blight in chickpea are poorly understood. We used a blight-resistant (HC1) and a blight-susceptible (GPF2) genotype of chickpea and genes of pathogenesis-related proteins (PRPs), phenylpropanoid pathway metabolites, abscisic acid (ABA), gibberellic acid (GA) and jasmonic acid (JA) to understand the role of these in A. rabiei resistance/susceptibility. The JA, ABA and GA biosynthesis genes of chickpea were retrieved, characterized and gene-specific primers were used for transcriptional studies. Gene expression revealed that chickpea activated its defences rather quickly and well before initiation of spore germination. In resistant HC1, the majority of the JA, GA and phenylpropanoid pathway genes had peak maxima at 2 h post-inoculation (hpi) whereas PRPs/defence genes had peak maxima at 24/36 hpi implying that defence to A. rabiei in chickpea is composed of a two-tier system separated by time: immediately after spore attachment and at or just prior to host penetration. Unlike HC1, susceptible GPF2 was late in activation of defence responses or did not activate them. Another striking difference between HC1 and GPF2 was up-regulation of ABA biosynthesis genes in inoculated GPF2 and down-regulation in HC1. This study revealed that phenylpropanoids, PRPs, JA, 8-(1R,2R)-3-oxo-2-(Z)-pent-2-enyl cyclopentyl octanoate, (15Z)-12-oxophyto-10,15-dienoic acid and methyl-jasmonate govern resistance to A. rabiei in chickpea whereas ABA governs susceptibility.
Transcriptional profiling identifies the early responses to Puccinia triticina infection in the adult plant leaf rust resistant wheat variety Toropi
The wheat cv. Toropi displays a durable leaf rust resistance that is associated with a prehaustorial resistance phenotype and rapid changes in wheat gene expression following Puccinia triticina inoculation.
Abstract
Leaf rust, caused by Puccinia triticina (Pt), is a major disease of wheat and a significant problem for wheat production in Brazil. The Brazilian variety Toropi, released in 1965, has maintained high levels of field, adult plant resistance (APR) to leaf rust across global locations, while microscopic studies have indicated prehaustorial resistance mechanisms. Analyses of gene expression in flag leaves of Toropi, during the early stages of Pt infection, were undertaken to explore the mechanisms behind the APR in Toropi. Differential expression of wheat genes was undertaken, comparing Pt- to mock-inoculated and Pt- to Pt-inoculated time points. Analysis of gene expression indicated a strong response to Pt, which was fully active by 6 h after inoculation (hai). More genes were downregulated than upregulated, particularly at 6 and 12 hai. Gene Ontology enrichment analysis indicated a shutting down of RNA and protein synthesis and an early effect on photosynthesis, with disruption of the electron transfer chain. Analyses of upregulated genes identified genes involved in ATP-binding and protein kinase activity at 6 hai, supporting a rapid metabolic response to Pt infection. A general upregulation of genes involved in transport and metabolism indicated the need to relocate protein and organic-based resources. Alignment of differentially expressed genes with the genomic regions defining four leaf rust APR quantitative trait loci (QTLs) in Toropi identified candidate resistance genes, including a sugar transporter, a receptor kinase and a seven-transmembrane MLO family protein. In addition, 60 Pt genes were identified, 11 being annotated as potential effector proteins.
Functional organic matter components in mangrove soils revealed by density fractionation
Effects of SNP marker density and training population size on prediction accuracy in alfalfa (Medicago sativa L.) genomic selection
Abstract
Effects of individual single-nucleotide polymorphism (SNP) markers and the size of “training” and “test” populations affect prediction accuracy in genomic selection (GS). This study evaluated 11 subsets of 4932 SNPs using six genetic additive methods to understand marker density in GS prediction in alfalfa (Medicago sativa L.). In the GS methods, the effect of “training” to “test” population size was also evaluated. Fourteen alfalfa populations sampled from long-term grazing sites were genotyped using genotyping by sequencing for the identification of SNPs. These populations were also phenotyped for six agromorphological and three nutritive traits from 2018 to 2020. The accuracy of GS prediction improved across six GS methods when the ratio of “training” to “test” population size increased. However, the prediction accuracy of the six GS methods reduced to a range of −0.27 to 0.11 when random, uninformative SNPs were used. In this study, five Bayesian methods and ridge-regression best linear unbiased prediction (rrBLUP) method had similar GS accuracies for “training” sets, but rrBLUP tended to outperform Bayesian methods in independent “test” sets when SNP subsets with high mean-squared-estimated-marker effect were used. These findings can enhance the application of GS in alfalfa genetic improvement.
Common signatures of selection reveal target loci for breeding across soybean populations
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.)
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.