TaCHP encoding C1-domain protein stably enhances wheat yield in saline-alkaline fields.

Overexpression of the zinc finger gene TaCHP stably enhanced wheat yield in saline-alkaline conditions in a multi-year, three-site field trial, and the genetic variations in its promoter contribute to saline-alkaline tolerance of wheat accessions. TaCHP and its tolerant haplotype have great potential for molecular breeding of stress-tolerant wheat.

Mapping Quantitative Trait Loci for Type II Fusarium Head Blight Resistance in Two Wheat Recombinant Inbred Line Populations Derived from Yangmai 4 and Yangmai 5.

Fusarium head blight (FHB) is a destructive wheat disease worldwide and significantly affects grain yield and quality in wheat. To understand the genetic basis underlying type II FHB resistance in two elite wheat cultivars-Yangmai 4 (YM4) and Yangmai 5 (YM5)-quantitative trait loci (QTL) mapping was conducted in two recombinant inbred line (RIL) populations derived from the crosses of YM4 and YM5 with susceptible cultivar Yanzhan 1 (YZ1), respectively. A survey with markers linked to Fhb1, Fhb2, Fhb4, and Fhb5 in landrace Wangshuibai indicated the nonexistence of these known FHB resistance genes or QTL in YM4, YM5, and YZ1. One overlapped resistance QTL was identified in both RIL populations (namely, QFhb.Y4.2D/QFhb.Y5.2D) with a large effect on FHB resistance. One novel resistance QTL (QFhb.Y4.5A) mapped on chromosome 5A was detected only in the YM4/YZ1 population. The resistance alleles of both QFhb.Y4.2D/QFhb.Y5.2D and QFhb.Y4.5A did not increase the plant height and did not significantly affect the heading date and flowering date. Kompetitive allele-specific PCR markers for QFhb.Y4.2D/QFhb.Y5.2D and QFhb.Y4.5A had been developed to verify in an additional set of 244 geographically diverse cultivars or lines. Pyramiding of the two resistance alleles decreased the percentage of symptomatic spikelets by 51.77% relative to the cultivars or lines without these two resistance alleles. QFhb.Y4.2D/QFhb.Y5.2D and QFhb.Y4.5A were shown to be useful alternatives in FHB resistance breeding programs. The results will facilitate marker-assisted selection for introgression of the favorable alleles for improving FHB resistance in breeding programs.

Identification of new resistance loci against wheat sharp eyespot through genome-wide association study.

Introduction: Wheat sharp eyespot caused by Rhizoctonia cerealis is a serious pathogenic disease affecting plants. The effective strategy for controlling this disease is breeding resistant cultivar. However, to date, no wheat varieties are fully resistant to sharp eyespot, and only a few quantitative trait loci (QTLs) have been shown to be associated with sharp eyespot resistance. Methods: To understand the genetic basis of this disease, a genome-wide association study (GWAS) of sharp eyespot resistance in 262 varieties from all China wheat regions was conducted. Results: After cultivation for three years, only 6.5% of the varieties were resistant to sharp eyespot. Notably, the varieties from the middle and lower Yangtze River displayed higher sharp eyespot resistance than those from Huanghuai wheat zone. Only two varieties had the same resistance level to the control Shanhongmai. The results of GWAS showed that 5 single nucleotide polymorphism (SNP) loci were markedly related to sharp eyespot resistance in the three years repeatedly, and two QTLs, qSE-6A and qSE-7B, on chromosome 6A and 7B were identified. Based on the 'CG' haplotypes of significant SNPs, we found that the two QTLs exhibited additive effects on attenuating sharp eyespot resistance. Discussion: These results provide novel insights into the genetic basis of sharp eyespot resistance in China wheat varieties. The SNPs related to sharp eyespot resistance can be applied for marker-assisted selection in plant breeding.

Effects of Different Fertilizer Treatments, Environment and Varieties on the Yield-, Grain-, Flour-, and Dough-Related Traits and Cookie Quality of Weak-Gluten Wheat.

Weak-gluten wheat is the main raw material for crisp and soft foods such as cookies, cakes, and steamed breads in China. However, it remains challenging to find an appropriate fertilization regime to balance the yield and quality of wheat for special uses (such as cookie making). Here, four nitrogen (N) fertilizer treatments were compared in terms of effects on the yield-, grain-, flour-, and dough-related traits and cookie quality of nine weak-gluten wheat varieties. Compared with other treatments, the treatment M (which had 180 kg ha-1 N fertilizers with basal fertilizer:tillering fertilizer:jointing fertilizer = 5:1:4) was a superior fertilization strategy as it could ensure a higher yield (4.46 kg block-1) and proper traits related to cookie quality. Moreover, environmental conditions and wheat genotypes exhibited significant effects on many quality-related traits. The quality of Chinese crisp biscuits showed a significant association with unit weight, redness, and solvent retention capacity in lactic acid solution, while that of American cookies was influenced by thousand-grain weight, hardness, rate of yield flour, and formation time as indicated by the Mantel test. Additional Pearson correlation analysis demonstrated that thousand-grain weight, hardness, and rate of yield flour can affect the quality of American cookies. Our findings demonstrate that it is necessary to comprehensively consider local conditions, variety selection, and optimal fertilization to achieve high-quality weak-gluten wheat for cookie making.

Identification of quantitative trait loci for Fusarium head blight (FHB) resistance in the cross between wheat landrace N553 and elite cultivar Yangmai 13.

Fusarium head blight (FHB) of wheat poses a serious threat to food security in the Yellow-Huai River Valley Winter Wheat Region (YHW) of China. Discovery of new resistant quantitative trait loci (QTLs) or genes and application of them to highly susceptible varieties in the YHW are of great significance for ensuring the grain yield. Here, 160 recombinant inbred lines (RILs) from the cross between N553 (resistant) and Yangmai 13 (moderately susceptible) were used to evaluate FHB resistance by point inoculation, spray inoculation, and natural infection. A high-density genetic map was constructed by using a 15K SNP array and 128 polymorphism SSR markers. A total of 1452 polymorphic markers were identified, which formed 21 linkage groups and covered a total of 3555.1 cM in length. Two and four QTLs respectively related to type I and type II resistance were detected, among which QFhb-hnau.3BS.1 and QFhb-hnau.2DL were stably identified in most environments in Yangzhou and Zhengzhou, whereas QFhbn-hnau.5AL was only identified under natural infection in Jianyang. Based on the physical position (IWGSC RefSeq v1.0), QFhb-hnau.3BS.1 from the landrace N553 is likely to be Fhb1, while QFhb-hnau.2DL from Yangmai 13 may be a novel QTL. Significantly higher FHB resistance was observed in the lines with both QFhb-hnau.3BS.1 and QFhb-hnau.2DL, indicating that these two QTLs have apparent additive effects, and the RILs harboring both the two QTLs may have great application potential for the improvement of FHB resistance in wheat breeding. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-021-01220-5.

Wheat heat tolerance is impaired by heightened deletions in the distal end of 4AL chromosomal arm.

Heat stress (HS) causes substantial damages to worldwide crop production. As a cool season crop, wheat (Triticum aestivum) is sensitive to HS-induced damages. To support the genetic improvement of wheat HS tolerance (HST), we conducted fine mapping of TaHST1, a locus required for maintaining wheat vegetative and reproductive growth under elevated temperatures. TaHST1 was mapped to the distal terminus of 4AL chromosome arm using genetic populations derived from two BC6 F6 breeding lines showing tolerance (E6015-4T) or sensitivity (E6015-3S) to HS. The 4AL region carrying TaHST1 locus was approximately 0.949 Mbp and contained the last 19 high confidence genes of 4AL according to wheat reference genome sequence. Resequencing of E6015-3S and E6015-4T and haplotype analysis of 3087 worldwide wheat accessions revealed heightened deletion polymorphisms in the distal 0.949 Mbp region of 4AL, which was confirmed by the finding of frequent gene losses in this region in eight genome-sequenced hexaploid wheat cultivars. The great majority (86.36%) of the 3087 lines displayed different degrees of nucleotide sequence deletions, with only 13.64% of them resembling E6015-4T in this region. These deletions can impair the presence and/or function of TaHST1 and surrounding genes, thus rendering global wheat germplasm vulnerable to HS or other environmental adversities. Therefore, conscientious and urgent efforts are needed in global wheat breeding programmes to optimize the structure and function of 4AL distal terminus by ensuring the presence of TaHST1 and surrounding genes. The new information reported here will help to accelerate the ongoing global efforts in improving wheat HST.

Genome-wide association mapping revealed syntenic loci QFhb-4AL and QFhb-5DL for Fusarium head blight resistance in common wheat (Triticum aestivum L.).

BACKGROUND: Fusarium head blight (FHB), primarily caused by Fusarium graminearum, is a major threat to wheat production and food security worldwide. Breeding stably and durably resistant cultivars is the most effective approach for managing and controlling the disease. The success of FHB resistance breeding relies on identification of an effective resistant germplasm. We conducted a genome-wide association study (GWAS) using the high-density wheat 90 K single nucleotide polymorphism (SNP) assays to better understand the genetic basis of FHB resistance in natural population and identify associated molecular markers. RESULTS: The resistance to FHB fungal spread along the rachis (Type II resistance) was evaluated on 171 wheat cultivars in the 2016-2017 (abbr. as 2017) and 2017-2018 (abbr. as 2018) growing seasons. Using Illumina Infinum iSelect 90 K SNP genotyping data, a genome-wide association study (GWAS) identified 26 loci (88 marker-trait associations), which explained 6.65-14.18% of the phenotypic variances. The associated loci distributed across all chromosomes except 2D, 6A, 6D and 7D, with those on chromosomes 1B, 4A, 5D and 7A being detected in both years. New loci for Type II resistance were found on syntenic genomic regions of chromsome 4AL (QFhb-4AL, 621.85-622.24 Mb) and chromosome 5DL (QFhb-5DL, 546.09-547.27 Mb) which showed high collinearity in gene content and order. SNP markers wsnp_JD_c4438_5568170 and wsnp_CAP11_c209_198467 of 5D, reported previously linked to a soil-borne wheat mosaic virus (SBWMV) resistance gene, were also associated with FHB resistance in this study. CONCLUSION: The syntenic FHB resistant loci and associated SNP markers identified in this study are valuable for FHB resistance breeding via marker-assisted selection.

Genome-Wide Identification and Expression Profiles of Late Embryogenesis-Abundant (LEA) Genes during Grain Maturation in Wheat (Triticum aestivum L.).

Late embryogenesis-abundant (LEA) genes play important roles in plant growth and development, especially the cellular dehydration tolerance during seed maturation. In order to comprehensively understand the roles of LEA family members in wheat, we carried out a series of analyses based on the latest genome sequence of the bread wheat Chinese Spring. 121 Triticum aestivum L. LEA (TaLEA) genes, classified as 8 groups, were identified and characterized. TaLEA genes are distributed in all chromosomes, most of them with a low number of introns (≤3). Expression profiles showed that most TaLEA genes expressed specifically in grains. By qRT-PCR analysis, we confirmed that 12 genes among them showed high expression levels during late stage grain maturation in two spring wheat cultivars, Yangmai16 and Yangmai15. For most genes, the peak of expression appeared earlier in Yangmai16. Statistical analysis indicated that expression level of 8 genes in Yangmai 16 were significantly higher than Yangmai 15 at 25 days after anthesis. Taken together, our results provide more knowledge for future functional analysis and potential utilization of TaLEA genes in wheat breeding.

Genetic Analysis of Fusarium Head Blight Resistance in CIMMYT Bread Wheat Line C615 Using Traditional and Conditional QTL Mapping.

Fusarium head blight (FHB) is a destructive wheat disease present throughout the world, and host resistance is an effective and economical strategy used to control FHB. Lack of adequate resistance resource is still a main bottleneck for FHB genetics and wheat breeding research. The synthetic-derived bread wheat line C615, which does not carry the Fhb1 gene, is a promising source of FHB resistance for breeding. A population of 198 recombinant inbred lines (RILs) produced by crossing C615 with the susceptible cultivar Yangmai 13 was evaluated for FHB response using point and spray inoculations. As the disease phenotype is frequently complicated by other agronomic traits, we used both traditional and multivariate conditional QTL mapping approaches to investigate the genetic relationships (at the individual QTL level) between FHB resistance and plant height (PH), spike compactness (SC), and days to flowering (FD). A linkage map was constructed from 3,901 polymorphic SNP markers, which covered 2,549.2 cM. Traditional and conditional QTL mapping analyses found 13 and 22 QTL for FHB, respectively; 10 were identified by both methods. Among these 10, three QTL from C615 were detected in multiple years; these QTL were located on chromosomes 2AL, 2DS, and 2DL. Conditional QTL mapping analysis indicated that, at the QTL level, SC strongly influenced FHB in point inoculation; whereas PH and SC contributed more to FHB than did FD in spray inoculation. The three stable QTL (QFhbs-jaas.2AL, QFhbp-jaas.2DS, and QFhbp-jaas.2DL) for FHB were partly affected by or were independent of the three agronomic traits. The QTL detected in this study improve our understanding of the genetic relationships between FHB response and related traits at the QTL level and provide useful information for marker-assisted selection for the improvement of FHB resistance in breeding.

Quantitative trait loci responsible for sharp eyespot resistance in common wheat CI12633.

Sharp eyespot is a major fungal disease of wheat caused by Rhizoctonia cerealis in cool and humid environments worldwide. In this study, 224 single seed descent derived F13, F14 and F15 recombinant inbred lines (RILs) from the cross between CI12633 (a resistant cultivar) and Yangmai 9 (a susceptible cultivar) were assessed for sharp eyespot resistance (R.cerealis isolate R0301) in field and greenhouse conditions in three growing seasons. Different agronomic characteristics were also evaluated in the field with no disease infection. All the lines were genotyped with the Illumina iSelect 90 K SNP wheat chip and 101 SSR markers. Sharp eyespot resistance was significantly negatively correlated with heading date and tiller angle, and significantly positively correlated with the diameter of the basal first internode and second internode. Five QTL with a likelihood of odds ratio score of higher than 3.0 were detected on chromosomes 2BS, 4BS, 5AL and 5BS, respectively. These identified QTL may be used in future wheat breeding programs through marker assisted selection for developing sharp eyespot resistant cultivars.

Characterization of a small GTP-binding protein gene TaRab18 from wheat involved in the stripe rust resistance.

The stripe rust resistance gene, Yr26, is commonly used in wheat production. Identification of Yr26 resistance related genes is important for better understanding of the resistance mechanism. TaRab18, a putative small GTP-binding protein, was screened as a resistance regulated gene as it showed differential expression between the Yr26-containing resistant wheat and the susceptible wheat at different time points after Pst inoculation. TaRab18 contains four typical domains (GI to GIV) of the small GTP-binding proteins superfamily and five domains (RabF1 to RabF5) specific to the Rab subfamily. From the phylogenetic tree that TaRab18 was identified as belonging to the RABC1 subfamily. Chromosome location analysis indicated that TaRab18 and its homeoalles were on the homeologous group 7 chromosomes, and the Pst induced TaRab18 was on the 7 B chromosome. Functional analysis by virus induced gene silencing (VIGS) indicated that TaRab18 was positively involved in the stripe rust resistance through regulating the hypersensitive response, and Pst can develop on the leaves of TaRab18 silenced 92R137. However, over-expression of TaRab18 in susceptible Yangmai158 did not enhance its resistance dramatically, only from 9 grade in Yangmai158 to 8 grade in the transgenic plant. However, histological observation indicated that the transgenic plants with over-expressed TaRab18 showed a strong hypersensitive response at the early infection stage. The research herein, will improve our understanding of the roles of Rab in wheat resistance.

A novel nitrogen-dependent gene associates with the lesion mimic trait in wheat.

KEY MESSAGE: Using bulk segregant analysis (BSA) coupling with RNA-seq and DNA markers identified a potentially novel nitrogen-dependent lesion mimic gene Ndhrl1 on 2BS in wheat. Lesion mimic (LM) refers to hypersensitive reaction-like (HRL) traits that appear on leaf tissue in the absence of plant pathogens. In a wheat line P7001, LM showed up on the leaves under the 0 g nitrogen (N) treatment, but disappeared when sufficient N was supplied, suggesting that LM is N-responsive and N dosage dependent. Using BSA strategy together with RNA-seq and DNA markers, we identified an N-dependent LM gene (Ndhrl1) and mapped it to the short arm of chromosome 2B using an F5 recombinant inbred population developed from the cross of P7001 × P216. The putative gene was delimited into an interval of 8.1 cM flanked by the CAPS/dCAPS markers 7hrC9 and 7hr2dc14, and co-segregated with the dCAPS marker 7hrdc2. This gene is most likely a novel gene for LM in wheat based on its chromosomal location. Further analysis of RNA-seq data showed that plant-pathogen interaction, nitrogen metabolism, zeatin biosynthesis and plant hormone signal transduction pathways were significantly differentially expressed between LM and non-LM lines.