Search

Processing quality is an important economic wheat trait. The marker-assisted selection (MAS) method plays a vital role in accelerating genetic improvement of processing quality. In the present study, processing quality in a panel of 165 cultivars grown in four environments was evaluated by mixograph. An association mapping analysis using 90 K and 660 K single nucleotide polymorphism (SNP) arrays identified 24 loci in chromosomes 1A, 1B (4), 1D, 2A, 2B (2), 3A, 3B, 3D (2), 4A (3), 4B, 5D (2), 6A, 7B (2) and 7D (2), explaining 10.2–42.5% of the phenotypic variances. Totally, 15 loci were stably detected in two or more environments. Nine loci coincided with known genes or QTL, whereas the other fifteen were novel loci. Seven candidate genes encoded 3-ketoacyl-CoA synthase, lipoxygenase, pyridoxal phosphate-dependent decarboxylase, sucrose synthase 3 and a plant lipid transfer protein/Par allergen. SNPs significantly associated with processing quality and accessions with more favorable alleles can be used for marker-assisted selection. [ABSTRACT FROM AUTHOR]

Background and Aims Physiological and morphological traits play essential roles in wheat (Triticum aestivum) growth and development. In particular, photosynthesis is a limitation to yield. Increasing photosynthesis in wheat has been identified as an important strategy to increase yield. However, the genotypic variations and the genomic regions governing morphological, architectural and photosynthesis traits remain unexplored. Methods Here, we conducted a large-scale investigation of the phenological, physiological, plant architectural and yield-related traits, involving 32 traits for 166 wheat lines during 2018–2020 in four environments, and performed a genome-wide association study with wheat 90K and 660K single nucleotide polymorphism (SNP) arrays. Key Results These traits exhibited considerable genotypic variations in the wheat diversity panel. Higher yield was associated with higher net photosynthetic rate (r = 0.41, P < 0.01), thousand-grain weight (r = 0.36, P < 0.01) and truncated and lanceolate shape, but shorter plant height (r = −0.63, P < 0.01), flag leaf angle (r = −0.49, P < 0.01) and spike number per square metre (r = −0.22, P < 0.01). Genome-wide association mapping discovered 1236 significant stable loci detected in the four environments among the 32 traits using SNP markers. Trait values have a cumulative effect as the number of the favourable alleles increases, and significant progress has been made in determining phenotypic values and favourable alleles over the years. Eleven elite cultivars and 14 traits associated with grain yield per plot (GY) were identified as potential parental lines and as target traits to develop high-yielding cultivars. Conclusions This study provides new insights into the phenotypic and genetic elucidation of physiological and morphological traits in wheat and their associations with GY, paving the way for discovering their underlying gene control and for developing enhanced ideotypes in wheat breeding. [ABSTRACT FROM AUTHOR]

Biofortification is a sustainable strategy to alleviate micronutrient deficiency in humans. It is necessary to improve grain zinc (GZnC) and iron concentrations (GFeC) in wheat based on genetic knowledge. However, the precise dissection of the genetic architecture underlying GZnC and GFeC remains challenging. In this study, high-resolution genome-wide association studies were conducted for GZnC and GFeC by three different models using 166 wheat cultivars and 373,106 polymorphic markers from the wheat 660K and 90K single nucleotide polymorphism (SNP) arrays. Totally, 25 and 16 stable loci were detected for GZnC and GFeC, respectively. Among them, 17 loci for GZnC and 8 for GFeC are likely to be new quantitative trait locus/loci (QTL). Based on gene annotations and expression profiles, 28 promising candidate genes were identified for Zn/Fe uptake (8), transport (11), storage (3), and regulations (6). Of them, 11 genes were putative wheat orthologs of known Arabidopsis and rice genes related to Zn/Fe homeostasis. A brief model, such as genes related to Zn/Fe homeostasis from root uptake, xylem transport to the final seed storage was proposed in wheat. Kompetitive allele-specific PCR (KASP) markers were successfully developed for two major QTL of GZnC on chromosome arms 3AL and 7AL, respectively, which were independent of thousand kernel weight and plant height. The 3AL QTL was further validated in a bi-parental population under multi-environments. A wheat multidrug and toxic compound extrusion (MATE) transporter TraesCS3A01G499300 , the ortholog of rice gene OsPEZ2 , was identified as a potential candidate gene. This study has advanced our knowledge of the genetic basis underlying GZnC and GFeC in wheat and provides valuable markers and candidate genes for wheat biofortification. [ABSTRACT FROM AUTHOR]

Stripe rust caused by Puccnina striiformis (Pst) is an economically important disease attacking wheat all over the world. Identifying and deploying new genes for Pst resistance is an economical and long-term strategy for controlling Pst. A genome-wide association study (GWAS) using single nucleotide polymorphisms (SNPs) and functional haplotypes were used to identify loci associated with stripe rust resistance in synthetic-derived (SYN-DER) wheats in four environments. In total, 92 quantitative trait nucleotides (QTNs) distributed over 65 different loci were associated with resistance to Pst at seedling and adult plant stages. Nine additional loci were discovered by the linkage disequilibrium-based haplotype-GWAS approach. The durable rust-resistant gene Lr34/Yr18 provided resistance in all four environments, and against all the five Pst races used in this study. The analysis identified several SYN-DER accessions that carried major genes: either Yr24/Yr26 or Yr32. New loci were also identified on chr2B, chr5B, and chr7D, and 14 QTNs and three haplotypes identified on the D-genome possibly carry new alleles of the known genes contributed by the Ae. tauschii founders. We also evaluated eleven different models for genomic prediction of Pst resistance, and a prediction accuracy up to 0.85 was achieved for an adult plant resistance, however, genomic prediction for seedling resistance remained very low. A meta-analysis based on a large number of existing GWAS would enhance the identification of new genes and loci for stripe rust resistance in wheat. The genetic framework elucidated here for stripe rust resistance in SYN-DER identified the novel loci for resistance to Pst assembled in adapted genetic backgrounds. [ABSTRACT FROM AUTHOR]

It is important to understand the genetic gain achieved through selection of key yield traits for planning future breeding strategies in developing high yielding wheat (Triticum aestivum L.) cultivars. The aim of this study was to characterize the genetic changes and genotype × environment (G×E) interaction by additive main effect and multiplicative interactions (AMMI) for morphological, physiological, and yield component traits under five environments using 24 wheat cultivars released from 1911 to 2016 in Pakistan. There was a significant increase in grain yield (9.03 kg ha−1 yr−1, 0.37%), and plant height was reduced linearly (−0.26 cm yr−1, −0.33%). The traits waxiness, leaf rolling, harvest index, spike length, and grains per spike significantly increased but the gain was only 0.16–0.2% per year. Analysis of variance revealed that genotype, environment, and G×E interaction were highly significant (P <.01) for all traits except relative chlorophyll content, biomass, days to maturity, and number of spikes. Gene‐specific markers identified the durable resistance gene Lr67/Yr46/Sr55/Pm46 in obsolete cultivars as early as 1911, whereas the photoperiod‐insensitive allele Ppd‐D1a and reduced height alleles Rht‐B1b and Rht‐D1b were present only in the post‐1965 cultivars. Diversity analysis based on a 50K single nucleotide polymorphism genotyping array clearly differentiated temporal patterns in 24 cultivars, which was correlated with the agronomic performance of the cultivars. This dataset provided detailed insight into the performance of historical wheat cultivars and could help in devising wheat breeding strategies to focus on the traits contributing to grain yield and have slower rate of genetic progress. Core Ideas: The genetic gain in morphology of Pakistani bread wheat cultivars over 105 yr areas was assessed.Leaf rolling, waxiness, and grains/spikes associated with genetic gains in grain yield were achieved by breeding.The performance and stability of yield and yield‐related traits was analyzed for the different cultivars. [ABSTRACT FROM AUTHOR]

Key message: A major QTL QTgw.caas-5B for thousand grain weight in wheat was fine mapped on chromosome 5B, and TraesCS5B02G044800 was predicted to be the candidate gene. Thousand grain weight (TGW), determined by grain length and width, and is an important yield component in wheat; understanding of the underlying genes and molecular mechanisms remains limited. A stable QTL QTgw.caas-5B for TGW was identified previously in a RIL population developed from a cross between Zhongmai 871 (ZM871) and a sister line Zhongmai 895 (ZM895), and the aim of this study was to perform fine mapping and validate the genetic effect of the QTL. It was delimited to an interval of approximately 2.0 Mb flanked by markers Kasp_5B29 and Kasp_5B31 (49.6–51.6 Mb) using 12 heterozygous recombinant plants obtained by selfing a residual BC1F6 line selected from the ZM871/ZM895//ZM871 population. A candidate gene was predicted following sequencing and differential expression analyses. Marker Kasp_5B_Tgw based on a SNP in TraesCS5B02G044800, the QTgw.caas-5B candidate, was developed and validated in a diversity panel of 166 cultivars. The precise mapping of QTgw.caas-5B laid a foundation for cloning of a predicted causal gene and provides a molecular marker for improving grain yield in wheat. [ABSTRACT FROM AUTHOR]

Preharvest sprouting (PHS) significantly reduces grain yield and quality. Identification of genetic loci for PHS resistance will facilitate breeding sprouting-resistant wheat cultivars. In this study, we constructed a genetic map comprising 1,702 non-redundant markers in a recombinant inbred line (RIL) population derived from cross Yangxiaomai/Zhongyou9507 using the wheat 15K single-nucleotide polymorphism (SNP) assay. Four quantitative trait loci (QTL) for germination index (GI), a major indicator of PHS, were identified, explaining 4.6–18.5% of the phenotypic variances. Resistance alleles of Qphs.caas-3AL, Qphs.caas-3DL , and Qphs.caas-7BL were from Yangxiaomai, and Zhongyou9507 contributed a resistance allele in Qphs.caas-4AL. No epistatic effects were detected among the QTL, and combined resistance alleles significantly increased PHS resistance. Sequencing and linkage mapping showed that Qphs.caas-3AL and Qphs.caas-3DL corresponded to grain color genes Tamyb10-A and Tamyb10-D , respectively, whereas Qphs.caas-4AL and Qphs.caas-7BL were probably new QTL for PHS. We further developed cost-effective, high-throughput kompetitive allele-specific PCR (KASP) markers tightly linked to Qphs.caas-4AL and Qphs.caas-7BL and validated their association with GI in a test panel of cultivars. The resistance alleles at the Qphs.caas-4AL and Qphs.caas-7BL loci were present in 72.2 and 16.5% cultivars, respectively, suggesting that the former might be subjected to positive selection in wheat breeding. The findings provide not only genetic resources for PHS resistance but also breeding tools for marker-assisted selection. [ABSTRACT FROM AUTHOR]

Background: Wheat is a momentous crop and feeds billions of people in the world. The improvement of wheat yield is very important to ensure world food security. Normal development of grain is the essential guarantee for wheat yield formation. The genetic study of grain phenotype and identification of key genes for grain filling are of great significance upon dissecting the molecular mechanism of wheat grain morphogenesis and yield potential. Results: Here we identified a pair of defective kernel (Dek) isogenic lines, BL31 and BL33, with plump and shrunken mature grains, respectively, and constructed a genetic population from the BL31/BL33 cross. Ten chromosomes had higher frequency of polymorphic single nucleotide polymorphism (SNP) markers between BL31 and BL33 using Wheat660K chip. Totally 783 simple sequence repeat (SSR) markers were chosen from the above chromosomes and 15 of these were integrated into two linkage groups using the genetic population. Genetic mapping identified three QTL, QDek.caas-3BS.1, QDek.caas-3BS.2 and QDek.caas-4AL, explaining 14.78–18.17%, 16.61–21.83% and 19.08–28.19% of phenotypic variances, respectively. Additionally, five polymorphic SNPs from Wheat660K were successfully converted into cleaved amplified polymorphic sequence (CAPS) markers and enriched the target regions of the above QTL. Biochemical analyses revealed that BL33 has significantly higher grain sucrose contents at filling stages and lower mature grain starch contents than BL31, indicating that the Dek QTL may be involved in carbohydrate metabolism. As such, the candidate genes for each QTL were predicated according to International Wheat Genome Sequence Consortium (IWGSC) RefSeq v1.0. Conclusions: Three major QTL for Dek were identified and their causal genes were predicted, laying a foundation to conduct fine mapping and dissect the regulatory mechanism underlying Dek trait in wheat. [ABSTRACT FROM AUTHOR]

Key message: Genetic diversity, population structure, LD decay, and selective sweeps in 687 wheat accessions were analyzed, providing relevant guidelines to facilitate the use of the germplasm in wheat breeding. Common wheat (Triticum aestivum L.) is one of the most widely grown crops in the world. Landraces were subjected to strong human-mediated selection in developing high-yielding, good quality, and widely adapted cultivars. To investigate the genome-wide patterns of allelic variation, population structure and patterns of selective sweeps during modern wheat breeding, we tested 687 wheat accessions, including landraces (148) and cultivars (539) mainly from China and Pakistan in a wheat 90 K single nucleotide polymorphism array. Population structure analysis revealed that cultivars and landraces from China and Pakistan comprised three relatively independent genetic clusters. Cultivars displayed lower nucleotide diversity and a wider average LD decay across whole genome, indicating allelic erosion and a diversity bottleneck due to the modern breeding. Analysis of genetic differentiation between landraces and cultivars from China and Pakistan identified allelic variants subjected to selection during modern breeding. In total, 477 unique genome regions showed signatures of selection, where 109 were identified in both China and Pakistan germplasm. The majority of genomic regions were located in the B genome (225), followed by the A genome (175), and only 77 regions were located in the D genome. EigenGWAS was further used to identify key selection loci in modern wheat cultivars from China and Pakistan by comparing with global winter wheat and spring wheat diversity panels, respectively. A few known functional genes or loci found within these genome regions corresponded to known phenotypes for disease resistance, vernalization, quality, adaptability and yield-related traits. This study uncovered molecular footprints of modern wheat breeding and explained the genetic basis of polygenic adaptation in wheat. The results will be useful for understanding targets of modern wheat breeding, and in devising future breeding strategies to target beneficial alleles currently not pursued. [ABSTRACT FROM AUTHOR]

Key message: We identified 21 new and stable QTL, and 11 QTL clusters for yield-related traits in three bread wheat populations using the wheat 90 K SNP assay.Abstract: Identification of quantitative trait loci (QTL) for yield-related traits and closely linked molecular markers is important in order to identify gene/QTL for marker-assisted selection (MAS) in wheat breeding. The objectives of the present study were to identify QTL for yield-related traits and dissect the relationships among different traits in three wheat recombinant inbred line (RIL) populations derived from crosses Doumai × Shi 4185 (D × S), Gaocheng 8901 × Zhoumai 16 (G × Z) and Linmai 2 × Zhong 892 (L × Z). Using the available high-density linkage maps previously constructed with the wheat 90 K iSelect single nucleotide polymorphism (SNP) array, 65, 46 and 53 QTL for 12 traits were identified in the three RIL populations, respectively. Among them, 34, 23 and 27 were likely to be new QTL. Eighteen common QTL were detected across two or three populations. Eleven QTL clusters harboring multiple QTL were detected in different populations, and the interval 15.5-32.3 cM around the Rht-B1 locus on chromosome 4BS harboring 20 QTL is an important region determining grain yield (GY). Thousand-kernel weight (TKW) is significantly affected by kernel width and plant height (PH), whereas flag leaf width can be used to select lines with large kernel number per spike. Eleven candidate genes were identified, including eight cloned genes for kernel, heading date (HD) and PH-related traits as well as predicted genes for TKW, spike length and HD. The closest SNP markers of stable QTL or QTL clusters can be used for MAS in wheat breeding using kompetitive allele-specific PCR or semi-thermal asymmetric reverse PCR assays for improvement of GY. [ABSTRACT FROM AUTHOR]

Key message: Four QTLs for adult-plant resistance to powdery mildew were mapped in the Zhou8425B/Chinese Spring population, and a new QTL on chromosome 3B was validated in 103 wheat cultivars derived from Zhou8425B.Abstract: Zhou8425B is an elite wheat (Triticum aestivum L.) line widely used as a parent in Chinese wheat breeding programs. Identification of genes for adult-plant resistance (APR) to powdery mildew in Zhou8425B is of high importance for continued controlling the disease. In the current study, the high-density Illumina iSelect 90K single-nucleotide polymorphism (SNP) array was used to map quantitative trait loci (QTL) for APR to powdery mildew in 244 recombinant inbred lines derived from the cross Zhou8425B/Chinese Spring. Inclusive composite interval mapping identified QTL on chromosomes 1B, 3B, 4B, and 7D, designated as QPm.caas-1BL.1, QPm.caas-3BS, QPm.caas-4BL.2, and QPm.caas-7DS, respectively. Resistance alleles at the QPm.caas-1BL.1, QPm.caas-3BS, and QPm.caas-4BL.2 loci were contributed by Zhou8425B, whereas that at QPm.caas-7DS was from Chinese Spring. QPm.caas-3BS, likely to be a new APR gene for powdery mildew resistance, was detected in all four environments. One SNP marker closely linked to QPm.caas-3BS was transferred into a semi-thermal asymmetric reverse PCR (STARP) marker and tested on 103 commercial wheat cultivars derived from Zhou8425B. Cultivars with the resistance allele at the QPm.caas-3BS locus had averaged maximum disease severity reduced by 5.3%. This STARP marker can be used for marker-assisted selection in improvement of the level of powdery mildew resistance in wheat breeding. [ABSTRACT FROM AUTHOR]

Background: Wheat genetic resources have been used for genetic improvement since 1876, when Stephen Wilson (Transactions and Proceedings of the Botanical Society of Edinburgh 12: 286) consciously made the first wide hybrid involving wheat and rye in Scotland. Wide crossing continued with sporadic attempts in the first half of 19th century and became a sophisticated scientific discipline during the last few decades with considerable impact in farmers' fields. However, a large diversity of untapped genetic resources could contribute in meeting future wheat production challenges. Perspectives and Conclusion: Recently the complete reference genome of hexaploid (Chinese Spring) and tetraploid (Triticum turgidum ssp. dicoccoides) wheat became publicly available coupled with on-going international efforts on wheat pan-genome sequencing. We anticipate that an objective appraisal is required in the post-genomics era to prioritize genetic resources for use in the improvement of wheat production if the goal of doubling yield by 2050 is to be met. Advances in genomics have resulted in the development of high-throughput genotyping arrays, improved and efficient methods of gene discovery, genomics-assisted selection and gene editing using endonucleases. Likewise, ongoing advances in rapid generation turnover, improved phenotyping, envirotyping and analytical methods will significantly accelerate exploitation of exotic genes and increase the rate of genetic gain in breeding. We argue that the integration of these advances will significantly improve the precision and targeted identification of potentially useful variation in the wild relatives of wheat, providing new opportunities to contribute to yield and quality improvement, tolerance to abiotic stresses, resistance to emerging biotic stresses and resilience to weather extremes. [ABSTRACT FROM AUTHOR]

Key message: We cloned TaSdr - A1 gene, and developed a gene-specific marker for TaSdr - A1 . A QTL for germination index at the TaSdr - A1 locus was identified in the Yangxiaomai/Zhongyou 9507 RIL population. Abstract: Pre-harvest sprouting (PHS) affects yield and end-use quality in bread wheat ( Triticum aestivum L.). In the present study we found an association between the TaSdr- A1 gene and PHS tolerance in bread wheat. TaSdr- A1 on chromosome 2A was cloned using a homologous cloning approach. Sequence analysis of TaSdr- A1 revealed an SNP at position 643, with the G allele being present in genotypes with lower germination index (GI) values and A in those with higher GI. These alleles were designated as TaSdr- A1a and TaSdr- A1b, respectively. A cleaved amplified polymorphism sequence (CAPS) marker Sdr2A based on the SNP was developed, and linkage mapping and QTL analysis were conducted to confirm the association between TaSdr- A1 and seed dormancy. Sdr2A was located in a 2.9 cM interval between SSR markers Xgwm95 and Xgwm372. A QTL for GI at the TaSdr- A1 locus explained 6.6, 7.3, and 8.2 % of the phenotypic variances in a Yangxiaomai/Zhongyou 9507 RIL population grown at Beijing, Shijiazhuang, and the averaged data from the two environments, respectively. Two sets of Chinese wheat cultivars used for validating the TaSdr- A1 polymorphism and the corresponding gene-specific marker Sdr2A showed that TaSdr- A1 was significantly associated with GI. Among 29 accessions with TaSdr- A1a, 24 (82.8 %) were landraces, indicating the importance of Chinese wheat landraces as sources of PHS tolerance. This study identified a novel PHS resistance allele TaSdr- A1a mainly presented in Chinese landraces and it is likely to be the causal gene for QPhs.ccsu- 2A.3, providing new information for an understanding of seed dormancy. [ABSTRACT FROM AUTHOR]

Key message : Nine QTL for black point resistance in wheat were identified using a RIL population derived from a Linmai 2/Zhong 892 cross and 90K SNP assay. Abstract: Black point, discoloration of the embryo end of the grain, downgrades wheat grain quality leading to significant economic losses to the wheat industry. The availability of molecular markers will accelerate improvement of black point resistance in wheat breeding. The aims of this study were to identify quantitative trait loci (QTL) for black point resistance and tightly linked molecular markers, and to search for candidate genes using a high-density genetic linkage map of wheat. A recombinant inbred line (RIL) population derived from the cross Linmai 2/Zhong 892 was evaluated for black point reaction during the 2011-2012, 2012-2013 and 2013-2014 cropping seasons, providing data for seven environments. A high-density linkage map was constructed by genotyping the RILs with the wheat 90K single nucleotide polymorphism (SNP) chip. Composite interval mapping detected nine QTL on chromosomes 2AL, 2BL, 3AL, 3BL, 5AS, 6A, 7AL (2) and 7BS, designated as QBp.caas- 2AL, QBp.caas- 2BL, QBp.caas- 3AL, QBp.caas- 3BL, QBp.caas- 5AS, QBp.caas- 6A, QBp.caas- 7AL.1, QBp.caas- 7AL.2 and QBp.caas- 7BS, respectively. All resistance alleles, except for QBp.caas- 7AL.1 from Linmai 2, were contributed by Zhong 892. QBp.caas- 3BL, QBp.caas- 5AS, QBp.caas- 7AL.1, QBp.caas- 7AL.2 and QBp.caas- 7BS probably represent new loci for black point resistance. Sequences of tightly linked SNPs were used to survey wheat and related cereal genomes identifying three candidate genes for black point resistance. The tightly linked SNP markers can be used in marker-assisted breeding in combination with the kompetitive allele specific PCR technique to improve black point resistance. [ABSTRACT FROM AUTHOR]

Stripe rust is one of the most devastating diseases of wheat (Triticum aestivum) worldwide. Adult-plant resistance (APR) is an efficient approach to provide long-term protection of wheat from the disease. The Chinese winter wheat cultivar Zhong 892 has a moderate level of APR to stripe rust in the field. To determine the inheritance of the APR resistance in this cultivar, 273 F6 recombinant inbred lines (RILs) were developed from a cross between Linmai 2 and Zhong 892. The RILs were evaluated for maximum disease severity (MDS) in two sites during the 2011–2012, 2012–2013 and 2013–2014 cropping seasons, providing data for five environments. Illumina 90k SNP (single nucleotide polymorphism) chips were used to genotype the RILs and their parents. Composite interval mapping (CIM) detected eight QTL, namely QYr.caas-2AL, QYr.caas-2BL.3, QYr.caas-3AS, QYr.caas-3BS, QYr.caas-5DL, QYr.caas-6AL, QYr.caas-7AL and QYr.caas-7DS.1, respectively. All except QYr.caas-2BL.3 resistance alleles were contributed by Zhong 892. QYr.caas-3AS and QYr.caas-3BS conferred stable resistance to stripe rust in all environments, explaining 6.2–17.4% and 5.0–11.5% of the phenotypic variances, respectively. The genome scan of SNP sequences tightly linked to QTL for APR against annotated proteins in wheat and related cereals genomes identified two candidate genes (autophagy-related gene and disease resistance gene RGA1), significantly associated with stripe rust resistance. These QTL and their closely linked SNP markers, in combination with kompetitive allele specific PCR (KASP) technology, are potentially useful for improving stripe rust resistances in wheat breeding. [ABSTRACT FROM AUTHOR]

The OsGS3 gene plays a principal role in controlling grain weight and grain length in rice. However, the function of an orthologous gene TaGS in wheat has not been analyzed to date. In the present study, we cloned the gDNA of TaGS gene, designated TaGS- D1, with four exons and three introns on chromosome 7DS by a comparative genomics approach. The cDNA of TaGS- D1 is 255 bp, and it encodes 85 amino acids. We also found a plant-specific organ size regulation domain in the deduced polypeptide, indicating that TaGS- D1, like OsGS3, does not belong to the PEBP family. DNA sequencing of the TaGS- D1 locus revealed no diversity in the coding sequence of exons, but there was a single nucleotide polymorphism (SNP) in the first intron, and 30 SNPs, a 40-bp InDel and a 3-bp InDel were found in the second intron between genotypes with higher and lower thousand grain weights (TGW). Based on the 40-bp InDel, a co-dominant STS marker, designated GS7D, was developed to discriminate the two alleles. GS7D was 8.0 cM from Xbarc184 located on chromosome 7DS by linkage mapping. A QTL for TGW and grain length at GS7D locus explained up to 16.3 and 7.7 %, respectively, of the phenotypic variances in a RIL population derived from Doumai/Shi 4185 grown in Shijiazhuang and Beijing. One hundred and seventy-five Chinese wheat cultivars were genotyped with GS7D, indicating that TaGS- D1 was significantly associated with grain weight. The allelic distribution at the TaGS- D1 locus showed that the frequencies of TaGS- D1a were high in cultivars from Serbia, Japan, Australia, Canada, and the Northeastern Spring Wheat and Northern Winter Wheat Regions of China. [ABSTRACT FROM AUTHOR]

Abstract: Meeting demands for increased cereal production in China is a great challenge and this paper provides updated information on cereal production and the potential adaptation of cropping systems to climate change, as well as on progress in improving yield potential and developing molecular markers and GM cereals in China. Maize production and soybean imports are increasing significantly to meet the strong demand for feed by a rapidly growing livestock industry. Extension of the rice and maize growing seasons in northeastern China and improvement of the cropping system through delayed wheat planting have contributed to improving cereal productivity despite changing climatic conditions. Significant improvements in yield potential of rice, maize, and wheat have been achieved. Comparative genomics has been successfully used to develop and validate functional markers for processing quality traits in wheat, and also for developing new varieties. Although transgenic Bt rice and maize, and maize expressing phytase have been developed, their commercialization has not been officially permitted. International collaboration has contributed significantly to cereal production by providing germplasm and improved crop management practices. Full integration of applied molecular technologies into conventional breeding programs and promotion of lower-input technologies, will play a key role in increasing and sustaining future cereal production. [Copyright &y& Elsevier]

Genome-wide association studies have identified multiple genetic variants associated with risk of esophageal squamous-cell carcinoma (ESCC) in Chinese populations. We examined whether these genetic factors, along with non-genetic factors, can contribute to ESCC risk prediction. We examined 25 single nucleotide polymorphisms (SNPs) and 4 non-genetic factors (sex, age, smoking and drinking) associated with ESCC risk in 9805 cases and 10 493 controls from Chinese populations. Weighted genetic risk score (wGRS) was calculated and logistic regression was used to analyze the association between wGRS and ESCC risk. We calculated the area under the curve (AUC) using receiver operating characteristic curve analysis to measure the discrimination after adding genetic variants to the model with only non-genetic factors. Net reclassification improvement (NRI) was used to quantify the degree of correct reclassification using different models. wGRS of the combined 17 SNPs with significant marginal effect (G SNPs) increased ~4-fold ESCC risk (P = 1.49 × 10−164) and the associations were significant in both drinkers and non-drinkers. However, wGRS of the eight SNPs with significant effect in gene × drinking interaction (GE SNPs) increased ~4-fold ESCC risk only in drinkers (Pinteraction = 8.76 × 10–41). The AUC for a risk model with 4 non-genetic factors, 17 G SNPs, 8 GE SNPs and their interactions with drinking was 70.1%, with the significant improvement of 7.0% compared with the model with only non-genetic factors (P < 0.0001). Our results indicate that incorporating genetic variants, lifestyle factors and their interactions in ESCC risk models can be useful for identifying patients with ESCC. [ABSTRACT FROM AUTHOR]

Background: Identification of loci for grain yield (GY) and related traits, and dissection of the genetic architecture are important for yield improvement through marker-assisted selection (MAS). Two genome-wide association study (GWAS) methods were used on a diverse panel of 166 elite wheat varieties from the Yellow and Huai River Valleys Wheat Zone (YHRVWD) of China to detect stable loci and analyze relationships among GY and related traits. Results: A total of 326,570 single nucleotide polymorphism (SNP) markers from the wheat 90 K and 660 K SNP arrays were chosen for GWAS of GY and related traits, generating a physical distance of 14,064.8 Mb. One hundred and twenty common loci were detected using SNP-GWAS and Haplotype-GWAS, among which two were potentially functional genes underpinning kernel weight and plant height (PH), eight were at similar locations to the quantitative trait loci (QTL) identified in recombinant inbred line (RIL) populations in a previous study, and 78 were potentially new. Twelve pleiotropic loci were detected on eight chromosomes; among these the interval 714.4–725.8 Mb on chromosome 3A was significantly associated with GY, kernel number per spike (KNS), kernel width (KW), spike dry weight (SDW), PH, uppermost internode length (UIL), and flag leaf length (FLL). GY shared five loci with thousand kernel weight (TKW) and PH, indicating significantly affected by two traits. Compared with the total number of loci for each trait in the diverse panel, the average number of alleles for increasing phenotypic values of GY, TKW, kernel length (KL), KW, and flag leaf width (FLW) were higher, whereas the numbers for PH, UIL and FLL were lower. There were significant additive effects for each trait when favorable alleles were combined. UIL and FLL can be directly used for selecting high-yielding varieties, whereas FLW can be used to select spike number per unit area (SN) and KNS. Conclusions: The loci and significant SNP markers identified in the present study can be used for pyramiding favorable alleles in developing high-yielding varieties. Our study proved that both GWAS methods and high-density genetic markers are reliable means of identifying loci for GY and related traits, and provided new insight to the genetic architecture of GY. [ABSTRACT FROM AUTHOR]

Alkylresorcinols (ARs), a group of phenolic lipids exclusively found in wheat, rye and barley among daily foods, are considered to be biomarkers for whole wheat grain intake. Recent studies have gradually revealed their functions and benefits for human health. However, the natural variation of ARs contents (ARC) in bread wheat cultivars in China has not been revealed. This study assayed grain ARC in a panel of 161 wheat cultivars grown in five environments in China and reports significant genotypic and environmental variation. Grain ARC ranged from 321 to 972 μg/g. Cultivars such as Yumai 18 and Yumai 2 had high ARC and thousand kernel weight (TKW) and can be utilized for production of ARs-fortified foods and as parents for breeding. Genome-wide association analysis with high-density single nucleotide polymorphism (SNP) arrays identified 24 and 32 stable loci associated with total ARC and thousand kernel ARC (TKAC), respectively. Loci on chromosome arms 3BL and 7BL, were significant for both ARC and TKAC. This study firstly revealed the extensive variation and genetic architecture of ARC in Chinese bread wheat, providing a theoretical basis for future high-ARC genetic improvement. [Display omitted] • Genotype and environment both contributes to extensive variation of grain ARC. • GWAS identified 32 and 24 stable loci based on ARC and TKAC, respectively. • Two loci were significant for ARC without sacrificing kernel weight. • Pyramiding favorable alleles of identified QTLs can increase grain ARC. [ABSTRACT FROM AUTHOR]

Ferulic acid is an important bioactive compound in wheat grains and has great effect on dietary health. Identification of genetic loci can facilitate breeding wheat cultivars with higher ferulic acid content (FAC). Here a genome-wide association study (GWAS) was conducted to identify genetic loci controlling FAC in wheat grain using 90K and 660K chips in a diversity panel of wheat cultivars. Eight major loci for FAC, FAC-1B , FAC-2A , FAC-4A-I , FAC-4A-II , FAC-6B , FAC-7B – I , FAC-7B - II and FAC-7B - III were detected and each explained approximately 10% of the phenotypic variances. The favorable alleles of the major loci have significantly accumulative effects on FAC. A group of varieties with more favorable alleles and higher FAC was also identified according to genotypic and phenotypic analyses. Two SNPs closely associated with FAC-4A-I and FAC-6B , respectively, were successfully converted to flexible kompetitive allele-specific PCR (KASP) markers to facilitate marker-assisted selection in breeding. The findings not only supply useable materials for food industry and breeding, but also lay a foundation for dissecting genetic architecture underpinning FAC in wheat. [Display omitted] • Identification of wheat genetic loci for ferulic acid content (FAC) facilitates breeding high-FAC varieties. • Major loci for FAC and wheat varieties with more favorable alleles and higher FAC were identified using SNP chips. • These outcomes dissected genetic architecture underpinning FAC and provided useable materials and tools for wheat high-FAC breeding. [ABSTRACT FROM AUTHOR]