Genome-wide linkage mapping of flour color-related traits and polyphenol oxidase activity in common wheat

Functional analysis of polyphenol oxidase 1 gene in common wheat

Polyphenol oxidase (PPO) activity is a major cause of the undesirable brown color of wheat-based products. Ppo1, a major gene for PPO activity, was cloned based on sequence homology in previous studies; however, its function and regulation mechanism remain unclear. In this study, the function and genetic regulation of Ppo1 were analyzed using RNA interference (RNAi) and Targeting Induced Local Lesions IN Genomes (TILLING) technology, and superior mutants were identified. Compared with the control, the level of Ppo1 transcript in RNAi transgenic lines was drastically decreased by 15.5%-60.9% during grain development, and PPO activity was significantly reduced by 12.9%-20.4%, confirming the role of Ppo1 in PPO activity. Thirty-two Ppo1 mutants were identified in the ethyl methanesulfonate (EMS)-mutagenized population, including eight missense mutations, 16 synonymous mutations, and eight intron mutations. The expression of Ppo1 was reduced significantly by 6.7%-37.1% and 10.1%-54.4% in mutants M092141 (G311S) and M091098 (G299R), respectively, in which PPO activity was decreased by 29.7% and 28.8%, respectively, indicating that mutation sites of two mutants have important effects on PPO1 function. Sequence and structure analysis revealed that the two sites were highly conserved among 74 plant species, where the frequency of glycine was 94.6% and 100%, respectively, and adjacent to the entrance of the hydrophobic pocket of the active site. The M092141 and M091098 mutants can be used as important germplasms to develop wheat cultivars with low grain PPO activity. This study provided important insights into the molecular mechanism of Ppo1 and the genetic improvement of wheat PPO activity.

Patterns of genetic variation and QTLs controlling grain traits in a collection of global wheat germplasm revealed by high-quality SNP markers

BACKGROUND

Establish a molecular breeding program involved assembling a diverse germplasm collection and generating accurate genotypes to characterize their genetic potential and associate them with agronomic traits. In this study, we acquired over eight hundred wheat accessions from international gene banks and assessed their genetic relatedness using high-quality SNP genotypes. Understanding the scope of genomic variation in this collection allows the breeders to utilize the genetic resources efficiently while improving wheat yield and quality.

RESULTS

A wheat diversity panel comprising 39 durum wheat, 60 spelt wheat, and 765 bread wheat accessions was genotyped on iSelect 90 K wheat SNP arrays. A total of 57,398 SNP markers were mapped to IWGSC RefSeq v2.1 assembly, over 30,000 polymorphic SNPs in the A, B, D genomes were used to analyze population structure and diversity, the results revealed the separation of the three species and the differentiation of CIMMYT improved breeding lines and landraces or widely grown cultivars. In addition, several chromosomal regions under selection were detected. A subset of 280 bread wheat accessions was evaluated for grain traits, including grain length, width, surface area, and color. Genome-wide association studies (GWAS) revealed that several chromosomal regions were significantly linked to known quantitative trait loci (QTL) controlling grain-related traits. One of the SNP peaks at the end of chromosome 7A was in strong linkage disequilibrium (LD) with WAPO-A1, a gene that governs yield components.

CONCLUSIONS

Here, the most updated and accurate physical positions of SNPs on 90 K genotyping array are provided for the first time. The diverse germplasm collection and associated genotypes are available for the wheat researchers to use in their molecular breeding program. We expect these resources to broaden the genetic basis of original breeding and pre-breeding materials and ultimately identify molecular markers associated with important agronomic traits which are evaluated in diverse environmental conditions.

Identification of genomic regions affecting grain peroxidase activity in bread wheat using genome-wide association study

BACKGROUND

Peroxidase (POD) activity plays an important role in flour-based product quality, which is mainly associated with browning and bleaching effects of flour. Here, we performed a genome-wide association study (GWAS) on POD activity using an association population consisted with 207 wheat world-wide collected varieties. Our study also provide basis for the genetic improvement of flour color-based quality in wheat.

RESULTS

Twenty quantitative trait loci (QTLs) were detected associated with POD activity, explaining 5.59-12.67% of phenotypic variation. Superior alleles were positively correlated with POD activity. In addition, two SNPs were successfully developed to KASP (Kompetitive Allele-Specific PCR) markers. Two POD genes, TraesCS2B02G615700 and TraesCS2D02G583000, were aligned near the QTLs flanking genomic regions, but only TraesCS2D02G583000 displayed significant divergent expression levels (P < 0.001) between high and low POD activity varieties in the investigated association population. Therefore, it was deduced to be a candidate gene. The expression level of TraesCS2D02G583000 was assigned as a phenotype for expression GWAS (eGWAS) to screen regulatory elements. In total, 505 significant SNPs on 20 chromosomes (excluding 4D) were detected, and 9 of them located within 1 Mb interval of TraesCS2D02G583000.

CONCLUSIONS

To identify genetic loci affecting POD activity in wheat grain, we conducted GWAS on POD activity and the candidate gene TraesCS2D02G583000 expression. Finally, 20 QTLs were detected for POD activity, whereas two QTLs associated SNPs were converted to KASP markers that could be used for marker-assisted breeding. Both cis- and trans-acting elements were revealed by eGWAS of TraesCS2D02G583000 expression. The present study provides genetic loci for improving POD activity across wide genetic backgrounds and largely improved the selection efficiency for breeding in wheat.

Playing with colours: genetics and regulatory mechanisms for anthocyanin pathway in cereals

Cereals form the most important source of energy in our food. Currently, demand for coloured food grains is significantly increasing globally because of their antioxidant properties and enhanced nutritional value. Coloured grains of major and minor cereals are due to accumulation of secondary metabolites like carotenoids and flavonoids such as anthocyanin, proanthocyanin, phlobaphenes in pericarp, aleurone, lemma, testa or seed coat of grains. Differential accumulation of colour in grains is regulated by several regulatory proteins and enzymes involved in flavonoid and caroteniod biosynthesis. MYB and bHLH gene family members are the major regulators of these pathways. Genes for colour across various cereals have been extensively studied; however, only a few functional and allele-specific markers to be utilized directly in breeding programmes are reported so far. In this review, while briefly discussing the well studied and explored carotenoid pathway, we focus on a much more complex anthocyanin pathway that is found across cereals. The genes and their orthologs that are responsible for encoding key regulators of anthocyanin biosynthesis are discussed. This review also focuses on the genetic factors that influence colour change in different cereal crops, and the available/reported markers that can be used in breeding programs for utilizing this pathway for enhancing food and nutritional security.

Genome wide association study of the whiteness and colour related traits of flour and dough sheets in common wheat

Flour whiteness and colour are important factors that influence the quality of wheat flour and end-use products. In this study, a genome wide association study focusing on flour and dough sheet colour using a high density genetic map constructed with 90K single nucleotide polymorphism arrays in a panel of 205 elite winter wheat accessions was conducted in two different locations in 2 years. Eighty-six significant marker-trait associations (MTAs) were detected for flour whiteness and the brightness index (L* value), the redness index (a* value), and the yellowness index (b* value) of flour and dough sheets (P < 10^-4) on homologous group 1, 2, 5 and 7, and chromosomes 3A, 3B, 4A, 6A and 6B. Four, three, eleven, eleven MTAs for the flour whiteness, L* value, a* value, b* value, and one MTA for the dough sheet L* value were identified in more than one environment. Based on MATs, some important new candidate genes were identified. Of these, two candidate genes, TraesCS5D01G004300 and Gsp-1D, for BS00000020_51 were found in wheat, relating to grain hardness. Other candidate genes were associated with proteins, the fatty acid biosynthetic process, the ketone body biosynthetic process, etc.

Development and validation of high-throughput and low-cost STARP assays for genes underpinning economically important traits in wheat

We developed and validated 56 gene-specific semi-thermal asymmetric reverse PCR (STARP) markers for 46 genes of important wheat quality, biotic and abiotic stress resistance, grain yield, and adaptation-related traits for marker-assisted selection in wheat breeding. Development of high-throughput, low-cost, gene-specific molecular markers is important for marker-assisted selection in wheat breeding. In this study, we developed 56 gene-specific semi-thermal asymmetric reverse PCR (STARP) markers for wheat quality, tolerance to biotic and abiotic stresses, grain yield, and adaptation-related traits. The STARP assays were validated by (1) comparison of the assays with corresponding diagnostic STS/CAPS markers on 40 diverse wheat cultivars and (2) characterization of allelic effects based on the phenotypic and genotypic data of three segregating populations and 305 diverse wheat accessions from China and 13 other countries. The STARP assays showed the advantages of high-throughput, accuracy, flexibility, simple assay design, low operational costs, and platform compatibility. The state-of-the-art assays of this study provide a robust and reliable molecular marker toolkit for wheat breeding programs.

Genome-Wide Association Mapping of Adult-Plant Resistance to Stripe Rust in Common Wheat (Triticum aestivum)

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a globally devastating disease of common wheat (Triticum aestivum L.), resulting in substantial economic losses. To identify effective resistance genes, a genome-wide association study was conducted on 120 common wheat lines from different wheat-growing regions of China using the wheat 90K iSelect SNP array. Seventeen loci were identified, explaining 9.5 to 21.8% of the phenotypic variation. Most of these genes were detected in the A (seven) and B (seven) genomes, with only three in the D genome. Among them, 11 loci were colocated with known resistance genes or quantitative trait loci reported previously, whereas the other six are likely new resistance loci. Annotation of flanking sequences of significantly associated SNPs indicated the presence of three important candidate genes, including E3 ubiquitin-protein ligase, F-box repeat protein, and disease resistance RPP13-like protein. This study increased our knowledge in understanding the genetic architecture for stripe rust resistance and identified wheat varieties with multiple resistance alleles, which are useful for improvement of stripe rust resistance in breeding.

Appraisal of wheat genomics for gene discovery and breeding applications: a special emphasis on advances in Asia

We discussed the most recent efforts in wheat functional genomics to discover new genes and their deployment in breeding with special emphasis on advances in Asian countries. Wheat research community is making significant progress to bridge genotype-to-phenotype gap and then applying this knowledge in genetic improvement. The advances in genomics and phenomics have intrigued wheat researchers in Asia to make best use of this knowledge in gene and trait discovery. These advancements include, but not limited to, map-based gene cloning, translational genomics, gene mapping, association genetics, gene editing and genomic selection. We reviewed more than 57 homeologous genes discovered underpinning important traits and multiple strategies used for their discovery. Further, the complementary advancements in wheat phenomics and analytical approaches to understand the genetics of wheat adaptability, resilience to climate extremes and resistance to pest and diseases were discussed. The challenge to build a gold standard reference genome sequence of bread wheat is now achieved and several de novo reference sequences from the cultivars representing different gene pools will be available soon. New pan-genome sequencing resources of wheat will strengthen the foundation required for accelerated gene discovery and provide more opportunities to practice the knowledge-based breeding.

QTL mapping for quality traits using a high-density genetic map of wheat

Protein- and starch-related quality traits, which are quantitatively inherited and significantly influenced by the environment, are critical determinants of the end-use quality of wheat. We constructed a high-density genetic map containing 10,739 loci (5,399 unique loci) using a set of 184 recombinant inbred lines (RILs) derived from a cross of 'Tainong 18 × Linmai 6' (TL-RILs). In this study, a quantitative trait loci (QTLs) analysis was used to examine the genetic control of grain protein content, sedimentation value, farinograph parameters, falling number and the performance of the starch pasting properties using TL-RILs grown in a field for three years. A total of 106 QTLs for 13 quality traits were detected, distributed on the 21 chromosomes. Of these, 38 and 68 QTLs for protein- and starch-related traits, respectively, were detected in three environments and their average values (AV). Twenty-six relatively high-frequency QTLs (RHF-QTLs) that were detected in more than two environments. Twelve stable QTL clusters containing at least one RHF-QTL were detected and classified into three types: detected only for protein-related traits (type I), detected only for starch-related traits (type II), and detected for both protein- and starch-related traits (type III). A total of 339 markers flanked with 11 QTL clusters (all except C6), were found to be highly homologous with 282 high confidence (HC) and 57 low confidence (LC) candidate genes based on IWGSC RefSeq v 1.0. These stable QTLs and RHF-QTLs, especially those grouped into clusters, are credible and should be given priority for QTL fine-mapping and identification of candidate genes with which to explain the molecular mechanisms of quality development and inform marker-assisted breeding in the future.

Multifamily QTL analysis and comprehensive design of genotypes for high-quality soft wheat

Milling properties and flour color are essential selection criteria in soft wheat breeding. However, high phenotypic screening costs restrict selection to relatively few breeding lines in late generations. To achieve marker-based selection of these traits in early generations, we performed genetic dissection of quality traits using three doubled haploid populations that shared the high-quality soft wheat variety Kitahonami as the paternal parent. An amplicon sequencing approach allowed effective construction of well-saturated linkage maps of the populations. Marker-based heritability estimates revealed that target quality traits had relatively high values, indicating the possibility of selection in early generations. Taking advantage of Chinese Spring reference sequences, joint linkage maps of the three populations were generated. Based on the maps, multifamily quantitative trait locus (QTL) analysis revealed a total of 86 QTLs for ten traits investigated. In terms of target quality traits, 12 QTLs were detected for flour yield, and 12 were detected for flour redness (a* value). Among these QTLs, six for flour yield and nine for flour a* were segregating in more than two populations. Some relationships among traits were explained by QTL collocations on chromosomes, especially group 7 chromosomes. Ten different ideotypes with various combinations of favorable alleles for the flour yield and flour a* QTLs were generated. Phenotypes of derivatives from these ideotypes were predicted to design ideal genotypes for high-quality wheat. Simulations revealed the possibility of breeding varieties with better quality than Kitahonami.

Genome-wide association study of six quality traits reveals the association of the TaRPP13L1 gene with flour colour in Chinese bread wheat

Flour colour, kernel hardness, grain protein content and wet gluten content are important quality properties that determine end use in bread wheat. Here, a wheat 90K genotyping assay was used for a genome-wide association study (GWAS) of the six quality-related traits in Chinese wheat cultivars in eight environments over four years. A total of 846 significant single nucleotide polymorphisms (SNPs) were identified, explaining approximately 30% of the phenotypic variation on average, and 103 multienvironment-significant SNPs were detected in more than four environments. Quantitative trait loci (QTL) mapping in the biparent population confirmed some important SNP loci. Moreover, it was determined that some important genes were associated with the six quality traits, including some known functional genes and annotated unknown functional genes. Of the annotated unknown functional genes, it was verified that TaRPP13L1 was associated with flour colour. Wheat cultivars or lines with TaRPP13L1-B1a showed extremely significantly higher flour redness and lower yellowness than those with TaRPP13L1-B1b in the Chinese wheat natural population and the doubled haploid (DH) population. Two tetraploid wheat lines with premature stop codons of the TaRPP13L1 gene mutagenized by ethyl methanesulfonate (EMS) showed extremely significantly higher flour redness and lower yellowness than wild type. Our data suggest that the TaRPP13L1 gene plays an important role in modulating wheat flour colour. This study provides useful information for further dissection of the genetic basis of flour colour and also provides valuable genes or genetic loci for marker-assisted selection to improve the process of breeding quality wheat in China.

Association Mapping for 24 Traits Related to Protein Content, Gluten Strength, Color, Cooking, and Milling Quality Using Balanced and Unbalanced Data in Durum Wheat [Triticum turgidum L. var. durum (Desf).]

Durum wheat [Triticum durum (Desf).] is mostly used to produce pasta, couscous, and bulgur. The quality of the grain and end-use products determine its market value. However, quality tests are highly resource intensive and almost impossible to conduct in the early generations in the breeding program. Modern genomics-based tools provide an excellent opportunity to genetically dissect complex quality traits to expedite cultivar development using molecular breeding approaches. This study used a panel of 243 cultivars and advanced breeding lines developed during the last 20 years to identify SNPs associated with 24 traits related to nutritional value and quality. Genome-wide association study (GWAS) identified a total of 179 marker-trait associations (MTAs), located in 95 genomic regions belonging to all 14 durum wheat chromosomes. Major and stable QTLs were identified for gluten strength on chromosomes 1A and 1B, and for PPO activity on chromosomes 1A, 2B, 3A, and 3B. As a large amount of unbalance phenotypic data are generated every year on advanced lines in all the breeding programs, the applicability of such a dataset for identification of MTAs remains unclear. We observed that ∼84% of the MTAs identified using a historic unbalanced dataset (belonging to a total of 80 environments collected over a period of 16 years) were also identified in a balanced dataset. This suggests the suitability of historic unbalanced phenotypic data to identify beneficial MTAs to facilitate local-knowledge-based breeding. In addition to providing extensive knowledge about the genetics of quality traits, association mapping identified several candidate markers to assist durum wheat quality improvement through molecular breeding. The molecular markers associated with important traits could be extremely useful in the development of improved quality durum wheat cultivars using marker-assisted selection (MAS).

Identification of a major QTL on chromosome arm 2AL for reducing yellow rust severity from a Chinese wheat landrace with evidence for durable resistance

A QTL on 2AL for reducing yellow rust severity was identified from a Chinese wheat landrace, being more effective than Yr18, with evidence for durable resistance from field observations. Utilization of wheat resistance is an important strategy to control yellow rust. The Chinese wheat landrace Hong Qimai (HQM) and the advanced breeding line AQ24788-83 (AQ; a progeny of HQM) can significantly reduce disease severity at the adult-plant growth stage. HQM has maintained adult-plant resistance for a prolonged period of time. To study the inheritance of the resistance, 126 recombinant inbred lines (RILs) derived from the cross Thatcher (TC) × HQM and 138 RILs from Luke × AQ were assessed for disease severity in six field trials. A genetic map of TC × HQM was constructed by genotyping these RILs using the 90 K wheat single-nucleotide polymorphism chip. Luke × AQ map was previously constructed for another disease study and also utilized here. Based on these maps and disease data, a quantitative trait locus (QTL) was detected on the chromosome arm 2AL from both TC × HQM and Luke × AQ and designated as QYr.cau-2AL. The resistance allele at QYr.cau-2AL came from HQM and AQ. QYr.cau-2AL was significantly effective across all the test environments and different genetic backgrounds, with its effect magnitude being higher than that of Yr18. QYr.cau-2AL synergistically acted with Yr18 and a QTL for high-temperature adult-plant resistance on 2BS, resulting in an elevated resistance from the juvenile plant growth stage onward, although QYr.cau-2AL alone displayed no substantial resistance at juvenile stage. Evidence indicates that QYr.cau-2AL is novel and confers durable resistance, and thus, should have high potential value for practical breeding.

Detection and validation of a novel major QTL for resistance to Fusarium head blight from Triticum aestivum in the terminal region of chromosome 7DL

A novel QTL for FHB resistance was mapped on wheat 7DL, being effective in multiple genetic backgrounds and environments, and comparable to Fhb1 in effect magnitude. Fusarium head blight (FHB) is one of the major fungal diseases affecting wheat production in many countries. The wheat line AQ24788-83 (AQ) possesses FHB resistance. The American wheat cultivar Luke is FHB susceptible. A Luke × AQ population consisting of 1652 advanced recombinant inbred lines (RILs) was developed, from which 272 RILs were randomly sampled and used to construct a linkage map. Another 154 RILs were selected for homogeneity in plant height (PH) and flowering date (FD). This selection strategy was adopted to reduce possible confounding effects on FHB assessment due to variation in PH and FD. The 272 and 154 RILs were genotyped applying simple sequence repeat (SSR), diversity arrays technology (DArT) and single-nucleotide polymorphism (SNP) markers. The two sets of RILs were evaluated for FHB resistance applying point inoculation in greenhouses; the 154 RILs were also evaluated applying spray inoculation in multiple field environments. The linkage map consisted of 2088 SSR, DArT, and SNP markers. A FHB resistance quantitative trait locus (QTL), designated as QFhb.cau-7DL, was detected on chromosome arm 7DL; this QTL was closely linked to the SSR marker gwm428 ( http://www.wheat.pw.usda.gov/ggpages/SSR/ ). QFhb.cau-7DL was significantly effective (α = 0.01) in every test trial, and its effectiveness was validated using three additional wheat crosses. Sumai 3 (donor wheat of the FHB resistance gene Fhb1) was used in one of these crosses. QFhb.cau-7DL was comparable to Fhb1 in effect magnitude, providing a great potential for improving FHB resistance.

Genome-wide linkage mapping of yield-related traits in three Chinese bread wheat populations using high-density SNP markers

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. 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.

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.

A Genome-Wide Association Study Reveals a Rich Genetic Architecture of Flour Color-Related Traits in Bread Wheat

Flour color-related traits, including brightness (L^*), redness (a^*), yellowness (b^*) and yellow pigment content (YPC), are very important for end-use quality of wheat. Uncovering the genetic architecture of these traits is necessary for improving wheat quality by marker-assisted selection (MAS). In the present study, a genome-wide association study (GWAS) was performed on a collection of 166 bread wheat cultivars to better understand the genetic architecture of flour color-related traits using the wheat 90 and 660 K SNP arrays, and 10 allele-specific markers for known genes influencing these traits. Fifteen, 28, 25, and 32 marker-trait associations (MTAs) for L^*, a^*, b^*, and YPC, respectively, were detected, explaining 6.5-20.9% phenotypic variation. Seventy-eight loci were consistent across all four environments. Compared with previous studies, Psy-A1, Psy-B1, Pinb-D1, and the 1B•1R translocation controlling flour color-related traits were confirmed, and four loci were novel. Two and 11 loci explained much more phenotypic variation of a^* and YPC than phytoene synthase 1 gene (Psy1), respectively. Sixteen candidate genes were predicted based on biochemical information and bioinformatics analyses, mainly related to carotenoid biosynthesis and degradation, terpenoid backbone biosynthesis and glycolysis/gluconeogenesis. The results largely enrich our knowledge of the genetic basis of flour color-related traits in bread wheat and provide valuable markers for wheat quality improvement. The study also indicated that GWAS was a powerful strategy for dissecting flour color-related traits and identifying candidate genes based on diverse genotypes and high-throughput SNP arrays.

Genome-wide association mapping of black point reaction in common wheat (Triticum aestivum L.)

BACKGROUND

Black point is a serious threat to wheat production and can be managed by host resistance. Marker-assisted selection (MAS) has the potential to accelerate genetic improvement of black point resistance in wheat breeding. We performed a genome-wide association study (GWAS) using the high-density wheat 90 K and 660 K single nucleotide polymorphism (SNP) assays to better understand the genetic basis of black point resistance and identify associated molecular markers.

RESULTS

Black point reactions were evaluated in 166 elite wheat cultivars in five environments. Twenty-five unique loci were identified on chromosomes 2A, 2B, 3A, 3B (2), 3D, 4B (2), 5A (3), 5B (3), 6A, 6B, 6D, 7A (5), 7B and 7D (2), respectively, explaining phenotypic variation ranging from 7.9 to 18.0%. The highest number of loci was detected in the A genome (11), followed by the B (10) and D (4) genomes. Among these, 13 were identified in two or more environments. Seven loci coincided with known genes or quantitative trait locus (QTL), whereas the other 18 were potentially novel loci. Linear regression showed a clear dependence of black point scores on the number of favorable alleles, suggesting that QTL pyramiding will be an effective approach to increase resistance. In silico analysis of sequences of resistance-associated SNPs identified 6 genes possibly involved in oxidase, signal transduction and stress resistance as candidate genes involved in black point reaction.

CONCLUSION

SNP markers significantly associated with black point resistance and accessions with a larger number of resistance alleles can be used to further enhance black point resistance in breeding. This study provides new insights into the genetic architecture of black point reaction.

Molecular Mapping of Reduced Plant Height Gene Rht24 in Bread Wheat

Height is an important trait related to plant architecture and yield potential in bread wheat (Triticum aestivum L.). We previously identified a major quantitative trait locus QPH.caas-6A flanked by simple sequence repeat markers Xbarc103 and Xwmc256 that reduced height by 8.0-10.4%. Here QPH.caas-6A, designated as Rht24, was confirmed using recombinant inbred lines (RILs) derived from a Jingdong 8/Aikang 58 cross. The target sequences of Xbarc103 and Xwmc256 were used as queries to BLAST against International Wheat Genome Sequence Consortium database and hit a super scaffold of approximately 208 Mb. Based on gene annotation of the scaffold, three gene-specific markers were developed to genotype the RILs, and Rht24 was narrowed to a 1.85 cM interval between TaAP2 and TaFAR. In addition, three single nucleotide polymorphism (SNP) markers linked to Rht24 were identified from SNP chip-based screening in combination with bulked segregant analysis. The allelic efficacy of Rht24 was validated in 242 elite wheat varieties using TaAP2 and TaFAR markers. These showed a significant association between genotypes and plant height. Rht24 reduced plant height by an average of 6.0-7.9 cm across environments and were significantly associated with an increased TGW of 2.0-3.4 g. The findings indicate that Rht24 is a common dwarfing gene in wheat breeding, and TaAP2 and TaFAR can be used for marker-assisted selection.

Genome-wide linkage mapping of QTL for black point reaction in bread wheat (Triticum aestivum L.)

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. 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.

Genetic analysis of phytoene synthase 1 (Psy1) gene function and regulation in common wheat

BACKGROUND

Phytoene synthase 1 (PSY1) is the most important regulatory enzyme in carotenoid biosynthesis, whereas its function is hardly known in common wheat. The aims of the present study were to investigate Psy1 function and genetic regulation using reverse genetics approaches.

RESULTS

Transcript levels of Psy1 in RNAi transgenic lines were decreased by 54-76 % and yellow pigment content (YPC) was reduced by 26-35 % compared with controls, confirming the impact of Psy1 on carotenoid accumulation. A series of candidate genes involved in secondary metabolic pathways and core metabolic processes responded to Psy1 down-regulation. The aspartate rich domain (DXXXD) was important for PSY1 function, and conserved nucleotides adjacent to the domain influenced YPC by regulating gene expression, enzyme activity or alternative splicing. Compensatory responses analysis indicated that three Psy1 homoeologs may be coordinately regulated under normal conditions, but separately regulated under stress. The period 14 days post anthesis (DPA) was found to be a key regulation node during grain development.

CONCLUSION

The findings define key aspects of flour color regulation in wheat and facilitate the genetic improvement of wheat quality targeting color/nutritional specifications required for specific end products.

Carotenoids in Staple Cereals: Metabolism, Regulation, and Genetic Manipulation

Carotenoids play a critical role in animal and human health. Animals and humans are unable to synthesize carotenoids de novo, and therefore rely upon diet as sources of these compounds. However, major staple cereals often contain only small amounts of carotenoids in their grains. Consequently, there is considerable interest in genetic manipulation of carotenoid content in cereal grain. In this review, we focus on carotenoid metabolism and regulation in non-green plant tissues, as well as genetic manipulation in staple cereals such as rice, maize, and wheat. Significant progress has been made in three aspects: (1) seven carotenogenes play vital roles in carotenoid regulation in non-green plant tissues, including 1-deoxyxylulose-5-phosphate synthase influencing isoprenoid precursor supply, phytoene synthase, β-cyclase, and ε-cyclase controlling biosynthesis, 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase and carotenoid cleavage dioxygenases responsible for degradation, and orange gene conditioning sequestration sink; (2) provitamin A-biofortified crops, such as rice and maize, were developed by either metabolic engineering or marker-assisted breeding; (3) quantitative trait loci for carotenoid content on chromosomes 3B, 7A, and 7B were consistently identified, eight carotenogenes including 23 loci were detected, and 10 gene-specific markers for carotenoid accumulation were developed and applied in wheat improvement. A comprehensive and deeper understanding of the regulatory mechanisms of carotenoid metabolism in crops will be beneficial in improving our precision in improving carotenoid contents. Genomic selection and gene editing are emerging as transformative technologies for provitamin A biofortification.

Genome-Wide QTL Mapping for Wheat Processing Quality Parameters in a Gaocheng 8901/Zhoumai 16 Recombinant Inbred Line Population

Dough rheological and starch pasting properties play an important role in determining processing quality in bread wheat (Triticum aestivum L.). In the present study, a recombinant inbred line (RIL) population derived from a Gaocheng 8901/Zhoumai 16 cross grown in three environments was used to identify quantitative trait loci (QTLs) for dough rheological and starch pasting properties evaluated by Mixograph, Rapid Visco-Analyzer (RVA), and Mixolab parameters using the wheat 90 and 660 K single nucleotide polymorphism (SNP) chip assays. A high-density linkage map constructed with 46,961 polymorphic SNP markers from the wheat 90 and 660 K SNP assays spanned a total length of 4121 cM, with an average chromosome length of 196.2 cM and marker density of 0.09 cM/marker; 6596 new SNP markers were anchored to the bread wheat linkage map, with 1046 and 5550 markers from the 90 and 660 K SNP assays, respectively. Composite interval mapping identified 119 additive QTLs on 20 chromosomes except 4D; among them, 15 accounted for more than 10% of the phenotypic variation across two or three environments. Twelve QTLs for Mixograph parameters, 17 for RVA parameters and 55 for Mixolab parameters were new. Eleven QTL clusters were identified. The closely linked SNP markers can be used in marker-assisted wheat breeding in combination with the Kompetitive Allele Specific PCR (KASP) technique for improvement of processing quality in bread wheat.