Zhonghu He

Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation

About 8,000 years ago in the Fertile Crescent, a spontaneous hybridization of the wild diploid grass Aegilops tauschii (2n = 14; DD) with the cultivated tetraploid wheat Triticum turgidum (2n = 4x = 28; AABB) resulted in hexaploid wheat (T. aestivum; 2n = 6x = 42; AABBDD). Wheat has since become a primary staple crop worldwide as a result of its enhanced adaptability to a wide range of climates and improved grain quality for the production of baker’s flour. Here we describe sequencing the Ae. tauschii genome and obtaining a roughly 90-fold depth of short reads from libraries with various insert sizes, to gain a better understanding of this genetically complex plant. The assembled scaffolds represented 83.4% of the genome, of which 65.9% comprised transposable elements. We generated comprehensive RNA-Seq data and used it to identify 43,150 protein-coding genes, of which 30,697 (71.1%) were uniquely anchored to chromosomes with an integrated high-density genetic map. Whole-genome analysis revealed gene family expansion in Ae. tauschii of agronomically relevant gene families that were associated with disease resistance, abiotic stress tolerance and grain quality. This draft genome sequence provides insight into the environmental adaptation of bread wheat and can aid in defining the large and complicated genomes of wheat species.

Wheat stripe rust in China

China has the largest stripe rust epidemic region in the world in terms of wheat acreage affected by the disease. Extensive studies on the epidemiology and management of stripe rust have been carried out since the widespread occurrence of the disease in the 1950s. Fifteen epidemic zones were classified, based on factors influencing the occurrence of wheat stripe rust. The disease can spread inter-regionally, mainly from west to east and from south to north. Winter-wheat growing regions in the north-west, south-west, and north, and spring-wheat growing regions in the north-west are the major epidemic areas. Hotspots of wheat stripe rust are mainly located in south-eastern Gansu and north-western Sichuan, and these areas constitute the inoculum base, centre of diversity, and major over-summering areas of the pathogen. Successful control in over-summering areas is the key to achieving sustainable management of stripe rust in China. Pathogen variability and race virulence have been monitored continuously, and the resistance genetics and background of Chinese wheat cultivars analysed. Effective management of stripe rust includes resistance breeding and application, diversification and deployment of various resistance genes, use of chemicals, adoption of appropriate agricultural practice, and integrated disease management in ‘hotspot’ regions. Collaboration of scientists among various organisations and disciplines is vital. We discuss the progress and challenges of wheat stripe rust management in China.

Composition of HMW and LMW glutenin subunits and their effects on dough properties, pan bread, and noodle quality of chinese bread wheats

ABSTRACT Knowledge of composition of high molecular weight glutenin subunits (HMW-GS) and low molecular weight glutenin subunits (LMW-GS) and their associations with pan bread and noodle quality will contribute to genetically improving processing quality of Chinese bread wheats. Two trials including a total of 158 winter and facultative cultivars and advanced lines were conducted to detect the allelic variation at Glu-1 and Glu-3 loci by SDS-PAGE electrophoresis and to understand their effects on dough properties, pan bread, and dry white Chinese noodle (DWCN) quality. Results indicate that subunits/alleles 1 and null at Glu-A1, 7+8 and 7+9 at Glu-B1, 2+12 and 5+10 at Glu-D1, alleles a and d at Glu-A3, and alleles j and d at Glu-B3 predominate in Chinese germplasm, and that 34.9% of the tested genotypes carry the 1B/1R translocation (allelic variation at Glu-D3 was not determined because no significant effects were reported previously). Both variations at HMW-GS and LMW-GS/alleles and loci interactions co...

Allelic variation at the Glu-1 and Glu-3 loci, presence of the 1B.1R translocation, and their effects on mixographic properties in Chinese bread wheats

Allelic variations at the Glu-1 and Glu-3 loci play an important role in determining dough properties and bread-making quality. Two hundred and fifty-one cultivars and advanced lines from four major Chinese wheat-producing zones in the autumn-sown wheat regions were used to investigate the high-molecular-weight glutenin subunits (HMW GS) and low-molecular-weight glutenin subunit (LMW GS) composition controlled by the Glu-1 and Glu-3 loci, respectively, as well as the presence of the 1B.1R translocation, and to determine the association of storage protein composition with protein content, SDS sedimentation value, and dough-mixing properties measured by mixograph. Three, nine, and four allelic variations were present at Glu-A1, Glu-B1, and Glu-D1, respectively. Subunits 1, N, 7+8, 7+9, and 2+12 are the dominant HMW GS, with frequencies of 51.3, 39.4, 38.2, 45.0, and 59.8%, respectively. Five and eight allelic variations were present at the Glu-A3 and Glu-B3 loci (data of Glu-D3 were not available), Glu-A3a, Glu-A3d, Glu-B3j (presence of the 1B.1R translocation), and Glu-B3d are the dominant LMW GS, with frequencies of 37.1, 31.7, 44.6, and 20.3%, respectively. The frequencies of allelic variation at Glu-1 and Glu-3 differ greatly in different regions. The effects of HMW GS and LMW GS on SDS sedimentation value, mixing time, and mixing tolerance were significant at P = 0.01, with Glu-D1 and Glu-B3 showing the largest contributions to mixing time and mixing tolerance. Averaged data from two locations showed that the quality effects of glutenin loci could be ranked as Glu-B3 > Glu-B1 > Glu-A1 > Glu-D1 > Glu-A3 for SDS sedimentation value, Glu-D1 > Glu-B3 > Glu-A1 = Glu-B1 = Glu-A3 for mixing time, and Glu-D1 > Glu-B3 = Glu-B1 > Glu-A3 > Glu-A1 for mixing tolerance, respectively. The significant and negative effect of the 1B.1R translocation on dough properties was confirmed. It was concluded that the high frequency of undesirable HMW GS and LMW GS and the presence of the 1B.1R translocation are responsible for the weak gluten property of Chinese germplasm; hence, reducing the frequency of the 1B.1R translocation and integration of desirable subunits at Glu-1 and Glu-3 such as 1, 7+8, 14+15, 5+10, Glu-A3d, and Glu-B3d, could lead to the improvement of gluten quality in Chinese wheats.

Functional markers in wheat: current status and future prospects

Functional markers (FM) are developed from sequence polymorphisms present in allelic variants of a functional gene at a locus. FMs accurately discriminate alleles of a targeted gene, and are ideal molecular markers for marker-assisted selection in wheat breeding. In this paper, we summarize FMs developed and used in common wheat. To date, more than 30 wheat loci associated with processing quality, agronomic traits, and disease resistance, have been cloned, and 97 FMs were developed to identify 93 alleles based on the sequences of those genes. A general approach is described for isolation of wheat genes and development of FMs based on in silico cloning and comparative genomics. The divergence of DNA sequences of different alleles that affect gene function is summarized. In addition, 14 molecular markers specific for alien genes introduced from common wheat relatives were also described. This paper provides updated information on all FMs and gene-specific STS markers developed so far in wheat and should facilitate their application in wheat breeding programs.

Molecular and biochemical characterization of puroindoline a and b alleles in Chinese landraces and historical cultivars

Kernel hardness that is conditioned by puroindoline genes has a profound effect on milling, baking and end-use quality of bread wheat. In this study, 219 landraces and 166 historical cultivars from China and 12 introduced wheats were investigated for their kernel hardness and puroindoline alleles, using molecular and biochemical markers. The results indicated that frequencies of soft, mixed and hard genotypes were 42.7, 24.3, and 33.0%, respectively, in Chinese landraces and 45.2, 13.9, and 40.9% in historical cultivars. The frequencies of PINA null, Pinb-D1b and Pinb-D1p genotypes were 43.8, 12.3, and 39.7%, respectively, in hard wheat of landraces, while 48.5, 36.8, and 14.7%, respectively, in historical hard wheats. A new Pinb-D1 allele, designated Pinb-D1t, was identified in two landraces, Guangtouxianmai and Hongmai from the Guizhou province, with the characterization of a glycine to arginine substitution at position 47 in the coding region of Pinb gene. Surprisingly, a new Pina-D1 allele, designated Pina-D1m, was detected in the landrace Hongheshang, from the Jiangsu province, with the characterization of a proline to serine substitution at position 35 in the coding region of Pina gene; it was the first novel mutation found in bread wheat, resulting in a hard endosperm with PINA expression. Among the PINA null genotypes, an allele designed as Pina-D1l, was detected in five landraces with a cytosine deletion at position 265 in Pina locus; while another novel Pina-D1 allele, designed as Pina-D1n, was identified in six landraces, with the characterization of an amino acid change from tryptophan-43 to a ‘stop’ codon in the coding region of Pina gene. The study of puroindoline polymorphism in Chinese wheat germplasm could provide useful information for the further understanding of the molecular basis of kernel hardness in bread wheat.

Pan bread and dry white chinese noodle quality in chinese winter wheats

Improvements in pan bread quality and Chinese dry white noodle (DWCN) quality are the major breeding objectives in the north China winter wheat region. Eighty-one wheat cultivars and advanced lines were sown in two locations in the 2000–2001 season to evaluate the quality of winter wheat germplasm and investigate the association between pan bread quality and DWCN quality. Significant variability was observed for grain, pan bread, and DWCN quality attributes. Six cultivars and lines showed very good pan bread quality, 23 showed excellent DWCN quality in both locations, and the cultivars Yumai 34 and Sunstate showed superior quality for both food products. Protein content and grain hardness were significantly associated with pan bread quality, while the gluten quality-related parameters SDS-sedimentation value, Farinograph stability, and Extensograph maximum resistance, were significantly associated with pan bread quality score, and accounted for 59.3–72.3% of its variation. Yellow colour (b, CIE Lab) showed a strong negative association with pan bread and DWCN quality largely due to the strong and negative association between yellow colour and gluten strength parameters in this germplasm pool. Flour ash content and polyphenol oxidase (PPO) had a negative moderate effect on noodle colour, while protein content and grain hardness were negatively associated with noodle colour, appearance, and smoothness. The association between SDS-sedimentation volume, Farinograph stability, and Extensograph maximum resistance and DWCN score fitted a quadratic regression model, accounting for 31.0%, 39.0%, and 47.0% of the DWCN score, respectively. The starch pasting parameters, peak viscosity and paste breakdown, contributed positively to DWCN quality, with r = 0.57 and 0.55, respectively. Quality requirements for pan bread and DWCN differ in colour, gluten strength, and pasting viscosity. It is suggested that PPO, yellow pigment, SDS sedimentation volume, and peak viscosity are parameters that could be used to screen for DWCN quality in the early generations of a wheat-breeding program.

Characterization of low-molecular-weight glutenin subunit Glu-B3 genes and development of STS markers in common wheat (Triticum aestivum L.)

Low-molecular-weight glutenin subunit (LMW-GS) Glu-B3 has a significant influence on the processing quality of the end-use products of common wheat. To characterize the LMW-GS genes at the Glu-B3 locus, gene-specific PCR primers were designed to amplify eight near-isogenic lines and Cheyenne with different Glu-B3 alleles (a, b, c, d, e, f, g, h and i) defined by protein electrophoretic mobility. The complete coding regions of four Glu-B3 genes with complete coding sequence were obtained and designated as GluB3-1, GluB3-2, GluB3-3 and GluB3-4. Ten allele-specific PCR markers designed from the SNPs present in the sequenced variants discriminated the Glu-B3 proteins of electrophoretic mobility alleles a, b, c, d, e, f, g, h and i. These markers were validated on 161 wheat varieties and advanced lines with different Glu-B3 alleles, thus confirming that the markers can be used in marker-assisted breeding for wheat grain processing quality.

Wheat genetic resources enhancement by the International Maize and Wheat Improvement Center (CIMMYT)

The International Maize and Wheat Improvement Center (CIMMYT) acts as a catalyst and leader in a global maize and wheat innovation network that serves the poor in the developing world. Drawing on strong science and effective partnerships, CIMMYT researchers create, share, and use knowledge and technology to increase food security, improve the productivity and profitability of farming systems and sustain natural resources. This people-centered mission does not ignore the fact that CIMMYT’s unique niche is as a genetic resources enhancement center for the developing world, as shown by this review article focusing on wheat. CIMMYT’s value proposition resides therefore in its use of crop genetic diversity: conserving it, studying it, adding value to it, and sharing it in enhanced form with clients worldwide. The main undertakings include: long-term safe conservation of world heritage of both crop resources for future generations, in line with formal agreements under the 2004 International Treaty on Plant Genetic Resources for Food and Agriculture, understanding the rich genetic diversity of two of the most important staples worldwide, exploiting the untapped value of crop genetic resources through discovery of specific, strategically-important traits required for current and future generations of target beneficiaries, and development of strategic germplasm through innovative genetic enhancement. Finally, the Center needs to ensure that its main products reach end-users and improve their livelihoods. In this regard, CIMMYT is the main international, public source of wheat seed-embedded technology to reduce vulnerability and alleviate poverty, helping farmers move from subsistence to income-generating production systems. Beyond a focus on higher grain yields and value-added germplasm, CIMMYT plays an “integrative” role in crop and natural resource management research, promoting the efficient use of water and other inputs, lower production costs, better management of biotic stresses, and enhanced system diversity and resilience.

Wheat quality traits and quality parameters of cooked dry white chinese noodles

Dry white Chinese noodle (DWCN) is widely consumed in China, and genetic improvement of DWCN quality has become a major objective for Chinese wheat breeding programs. One hundred and four bread wheat cultivars and advanced lines, including 88from major Chinese wheat-producing areas, were sown in two locations for two years. Their DWCN quality, as evaluated by trained panelists, was studied to determine the relationship between wheat quality parameters and DWCN quality attributes. In general, the cultivars and advanced lines used in this study are characterized with acceptable protein content, but accompanied with weak-medium gluten strength and poor extensibility, and substantial variation is observed for all grain and DWCN quality characters. On average, Australia and USA wheat performed better DWCN quality than Chinese wheats. Simple correlation analysis indicated that both grain hardness and Farinograph water absorption were negatively associated with cooked DWCN color, appearance, smoothness, and taste. Flour whiteness and RVA peak viscosity was positively associated with all DWCN parameters, and their correlation coefficients (r) with DWCN score are 0.34 and 0.41, respectively. Their positive contributions to DWCN quality were mostly through improved color, appearance, smoothness, and taste. Farinograph mixing tolerance index (MTI) and softening were negatively associated with all DWCN quality parameters, and their correlation coefficients with DWCN score are –0.50 and–0.54, respectively. Further analysis indicated that association between protein content, Zeleny sedimentation value, Farinograph stability, and Extensograph extensibility, and DWCN score fit quadratic regression model significantly, with R2 0.12, 0.32, 0.22, and 0.20, respectively. The associations between Zeleny sedimentation value and DWCNs appearance and taste also fit quadratic regression model significantly. This suggests that to certain extent, increased protein content and gluten quality contribute positively to DWCN quality, mostly by improving palatability, elasticity, and stickiness. High flour whiteness, medium protein content, medium to strong gluten strength and good extensibility, and high starch peak viscosity are desirable for DWCN quality. Genetic improvement for flour whiteness, protein quality and starch paste viscosity would increase the DWCN quality of Chinese bread wheat cultivars.