Characterization of a 4.1 Mb inversion harboring the stripe rust resistance gene YR86 on wheat chromosome 2AL

Wheat cultivar Zhongmai 895 was earlier found to carry YR86 in an 11.6 Mb recombination-suppressed region on chromosome 2AL when crossed with Yangmai 16.To fine-map the YR86 locus,we developed two large F2 populations from crosses Emai 580/Zhongmai 895 and Avocet S/Zhongmai 895.Remarkably,both populations exhibited suppressed recombination in the same 2AL region.Collinearity analysis across Chinese Spring,Aikang 58,and 10+wheat genomes revealed a 4.1 Mb chromosomal inversion spanning 708.5-712.6 Mb in the Chinese Spring reference genome.Molecular markers were developed in the breakpoint and were used to assess a wheat cultivar panel,revealing that Chinese Spring,Zhongmai 895,and Jimai 22 shared a common sequence named InvCS,whereas Aikang 58,Yangmai 16,Emai 580,and Avocet S shared the sequence named InvAK58.The inverted configuration explained the suppressed recombination observed in all three bi-parental populations.Normal recombination was observed in a Jimai 22/Zhongmai 895 F2 population,facilitating mapping of YR86 to a genetic interval of 0.15 cM corresponding to 710.27-712.56 Mb falling within the inverted region.Thirty-three high-confidence genes were annotated in the interval using the Chinese Spring reference genome,with six identified as potential candidates for YR86 based on genome and transcriptome analyses.These results will accelerate map-based cloning of YR86 and its deployment in wheat breeding.

Wheat stripe rust resistance gene Yr24/Yr26：A retrospective review

The objective of this review is to describe events in China and elsewhere that are related to the discovery, genetic identification, use, and ultimate break-down of a single wheat gene for resistance to stripe rust, namely Yr24/Yr26. In our retrospective analysis there was an early assumption of at least three genes at or near the locus, which caused an erroneous presumption of genetic diversity for resistance. It is an example of another boom and bust cycle in plant breeding with races virulent to Yr26(V26 races) now being the majority race group in the Chinese Pst population. We have attempted to present our story in a historical and personal context demonstrating research inputs from different national and international groups, as well as some significant contemporary side issues. It covers the period from the late 1980 s to 2017, during which significant rapid advances in the molecular biology of host: pathogen genetics occurred. We attempt to describe both successes and drawbacks in our work.

Haplotype variations in QTL for salt tolerance in Chinese wheat accessions identified by marker-based and pedigree-based kinship analyses

Most modern wheat cultivars were selected on the basis of yield-related indices measured under optimal fertilizer and irrigation inputs.With climate change,land degradation and salinity caused by sea water encroachment,wheat is increasingly subjected to environmental stress.Moreover,expanding urbanization increasingly encroaches upon prime agricultural land in countries like China,and alternative cropping areas must be found.Some of these areas have moderate constraining factors,such as salinity.Therefore,it is important to investigate whether current genetic materials and breeding procedures are maintaining adequate variability to address future problems caused by abiotic stress.In this study,a panel of 307 wheat accessions,including local landraces,exotic cultivars used in Chinese breeding programs and Chinese cultivars released during different periods since1940,were subjected to a genome-wide association study to dissect the genetic basis of salinity tolerance.Both marker-based and pedigree-based kinship analyses revealed that favorable haplotypes were introduced in some exotic cultivars as well as a limited number of Chinese landraces from the 1940 s.However,improvements in salinity tolerance during modern breeding are not as obvious as that of yield.To broaden genetic diversity for increasing salt tolerance,there is a need to refocus attention on local landraces that have high degrees of salinity tolerance and carry rare favorable alleles that have not been exploited in breeding.

SNP-based linkage mapping for validation of adult plant stripe rust resistance QTL in common wheat cultivar Chakwal 86

Wheat crops in China are constantly challenged by stripe rust. Deployment of cultivars with diverse resistances is the best strategy to control the disease. A recombinant inbred line(RIL) population derived from a cross between the resistant cultivar Chakwal 86 and susceptible landrace Mingxian 169 was studied in multiple environments to examine the underlying genetics and to identify quantitative trait loci(QTL) for stripe rust resistance.One hundred and twenty-eight RILs were genotyped with wheat 35 K SNP array and a genome-wide linkage map with 1480 polymorphic SNP markers, or bins, was constructed.Two major QTL on chromosomes 1BL and 3BS, and one minor QTL on 6BS had significant effects in reducing stripe rust severity. The QTL were validated using composite interval mapping(CIM) and inclusive composite interval mapping(ICIM). These methods explained59.0%–74.1% of the phenotype variation in disease response. The QTL on chromosome 1 BL was confirmed to be Yr29/Lr46 and the one on 3BS was the resistance allele identified in CIMMYT germplasm but was not Yr30/Sr2. The QTL on 6BS probably corresponded to previously known QTL. RILs with combined QTL were more resistant than those with single or no QTL. Kompetitive allele-specific PCR(KASP) assays for the QTL with largest effect QTL on chromosome 3BS were performed on a subset of RILs and 150 unrelated wheat lines. The QTL on 3BS with its linked KASP markers can be used in marker-assisted selection to improve stripe rust resistance in breeding programs.

Combined linkage and association mapping reveals two major QTL for stripe rust adult plant resistance in Shaanmai 155 and their haplotype variation in common wheat germplasm

The development and deployment of diverse resistance sources in new wheat cultivars underpin the durable control of stripe rust.In the present study,two loci for adult plant resistance(APR),QYr SM155.1 and QYr SM155.2,were identified in the Chinese wheat breeding line Shaanmai 155.QYr SM155.1 was mapped to a 3.0-c M interval between the single-nucleotide polymorphism(SNP)markers AX-109583610 and AX-110907562 on chromosome arm 2 BL.QYr SM155.2 was mapped to a 2.1-c M interval flanked by the SNP markers AX-110378556 and AX-86173526 on chromosome arm 7 AS.A genome-wide association study was used to identify markers associated with APR in a panel of 411 spring wheat lines.Thirteen and 11 SNPs were significantly associated with QYr SM155.1 and QYr SM155.2,respectively,corresponding to physical intervals of 653.75–655.52 Mb on 2 BL and 81.63–83.93 Mb on7 AS.To characterize the haplotype variation and the distribution of these QTL,haplotype analysis was performed based on these SNPs in an independent panel of 1101 worldwide wheat accessions.Three major haplotypes(2 B_h1,2 B_h2,and 2 B_h3)for QYr SM155.1 and four major haplotypes(7 A_h1,7 A_h2,7 A_h3,and 7 A_h4)for QYr SM155.2 were identified.Accessions individually harboring QYr SM155.1_h1 and QYr SM155.2_h1 haplotypes and their combination displayed resistance.Additional assays of 1306 current Chinese cultivars and breeding lines using markers flanking QYr SM155.1 and QYr SM155.2 indicated that the resistance haplotypes of the two QTL were present in respectively 1.45%and 14.16%of lines.Increasing resistance haplotype frequencies at these two loci using marker-assisted selection should benefit wheat production in China.

Using UAV-Based Temporal Spectral Indices to Dissect Changes in the Stay-Green Trait in Wheat

Stay-green(SG)in wheat is a beneficial trait that increases yield and stress tolerance.However,conventional phenotyping techniques limited the understanding of its genetic basis.Spectral indices(SIs)as non-destructive tools to evaluate crop temporal senescence provide an alternative strategy.Here,we applied Sls to monitor the senescence dynamics of 565 diverse wheat accessions from anthesis to maturation stages over 2 field seasons.Four Sis(normalized difference vegetation index,green normalized difference vegetation index,normalized difference red edge index,and optimized soil-adjusted vegetation index)were normalized to develop relative stay-green scores(RSGS)as the SG indicators.An RSGS-based genome-wide association study identified 47 high-confidence quantitative trait loci(QTL)harboring 3,079 single-nucleotide polymorphisms associated with SG and 1,085 corresponding candidate genes.Among them,15 QTL overlapped or were adjacent to known SG-related QTL/genes,while the remaining QTL were novel.Notably,a set of favorable haplotypes of SG-related candidate genes such as TraesCS2A03G1081100,TracesCS6B03G0356400,and TracesCS2B03G1299500 are increasing following the Green Revolution,further validating the feasibility of the pipeline.This study provided a valuable reference for further quantitative SG and genetic research in diverse wheat panels.

WHEAT STRIPE RUST AND INTEGRATION OF SUSTAINABLE CONTROL STRATEGIES IN CHINA

Stripe (yellow) rust caused by Puccinia striiformis f. sp. tritici occurs in almost allwheat-producing regions of the world. Severe countrywide epidemics in Chinahave caused substantial yield losses. Growing resistant cultivars is the beststrategy to control this disease but the pathogen can overcome resistance inwheat cultivars. The high variation in the virulence of the pathogen combinedwith the large areas of susceptible wheat cultivars enables the pathogenpopulation to increase rapidly and disperse over long distances under favorableenvironmental conditions, resulting in severe pandemics within croppingseasons. Current stripe rust control measures are based on many years ofresearch including the underlying epidemiology regarding year-to-year survivalof the pathogen, pathways of pathogen dispersal within seasons and years, therole of P. striiformis sexual hybridization, the use of resistance sources inbreeding programs, and year-round surveillance of national wheat crops that arepresent in different parts of the country throughout the year. All these strategiesdepend on accurate prediction of epidemics, more precise use of fungicides tomeet national requirements and better deployment of resistance genes. Newideas with potential application in sustainable protection of stripe rust includenegative regulatory gene editing, resistance gene overexpression and biologicalcontrol based on microbiomes.