Functional markers in wheat: current status and future prospects

Identification of stay-green candidate gene TaTRNH1-3B and development of molecular markers related to chlorophyll content and yield in wheat (Triticum aestivum L.)

Functional stay-green characteristic is closely associated with delayed loss in photosynthetic function and increased crop yield. However, the development and application of functional molecular markers based on stay-green-related genes are limited. This study compared and analyzed the differences of SPAD values, photosynthetic parameters, fluorescence parameters, and antioxidant enzyme activities at 0, 10, 18, 22, 26, 30 and 34 days after anthesis, as well as agronomic traits at mature stage between a stay-green line, Tailv113 (TL113), and a non-stay-green cultivar, Jinmai39 (JM39). The results showed that TL113 had higher photosynthetic capacity, photosynthetic efficiency, antioxidant capacity and yield than JM39. Subsequently, a comparative transcriptome analysis was conducted on TL113 and JM39 at 0, 26, and 30 days after anthesis. Analysis showed that senescence-associated co-expressed genes (SCEGs) and stay-green-associated differentially expressed genes (SDEGs) jointly affected wheat leaf senescence, while SDEGs played an important role in the stay green differences between TL113 and JM39. By analyzing the SNP sites of the SDEGs from transcriptome sequencing, a nsSNP was found in the TaTRNH1-3B sequence between TL113 and JM39. Further analyzing the resequencing data published in the Wheat Union database, four linked SNP sites were identified in TaTRNH1-3B, which formed two haplotypes, TaTRNH1-3B-Hap1 and TaTRNH1-3B-Hap2. Based on the SNP at 373 bp (A/G), a CAPS molecular marker, TaTRNH1-3B-Nla III-CAPS, was developed to distinguish allelic variations (A/G). Association analysis between TaTRNH1-3B allelic variation and agronomic traits found that the accessions possessing TaTRNH1-3B-Hap1 (A) exhibited significantly higher SPAD values than those possessing TaTRNH1-3B-Hap2 (G) in 6 of 10 environments at the jointing stage and in 7 of 10 environments at the grain filling stage in Beijing. Similarly, the accessions possessing TaTRNH1-3B-Hap1 (A) exhibited significantly higher chlorophyll contents and yield than those possessing TaTRNH1-3B-Hap2 (G) in 3 environments in Taigu. Additionally, lines with TaTRNH1-3B-Hap1 (A) displayed higher SPAD values at 0, 15, and 20 days after anthesis in the two BC3F3 populations than those with TaTRNH1-3B-Hap2 (G). These results suggest that TaTRNH1-3B is associated with the stay-green and yield traits in wheat, and TaTRNH1-3B-Hap1 is a favorable stay-green haplotype. The newly developed molecular marker, TaTRNH1-3B-Nla III-CAPS, provide valuable information for wheat genetic improvement of stay-green and high-yield traits, and can be used to marker-assisted selection breeding.

InDel Markers for Identifying Interspecific Hybrid Offspring of Apple and Pear

Distant hybridization, such as between apple (Malus domestica Borkh.) and pear (Pyrus communis L.), can introduce unique genetic traits that aren't possible through traditional hybridization methods. However, these hybrids often display maternal traits, making it difficult to visually identify hybrid offspring in the early stages. Thus, identifying these hybrids has been a longstanding challenge. To address this challenge, this study performed whole-genome resequencing of apple 'Golden Delicious' and pear 'Yan Zhuang', along with 62 of their hybrid offspring, to develop effective molecular markers. Genomic variation analysis revealed significant genetic diversity between apple and pear. By selecting markers based on notable parental differences and high polymorphism among offspring, 51 effective markers were identified from 340 apple-specific InDel markers. These markers could reliably identify the 62 offspring as distant hybrids with genetic material from both apple and pear. Among them, InDel1-7, InDel2-3, InDel3-1, and InDel4-3 proved to be the most efficient, achieving a 100% identification rate for hybrid offspring when used in combination in the 'Golden Delicious' × 'Yan Zhuang' population. Furthermore, marker universality tests showed that 88.2%, 76.5%, and 70.6% of the 51 markers were transferable to the 'Golden Delicious' × 'Jin Zhui', 'Fuji' × 'Yan Zhuang', and 'Fuji' × 'Jin Zhui' hybrid populations, respectively. The identification efficiencies in these three validation populations were 82.6%, 80.3%, and 85.0%, with the four highly efficient markers exceeding a 70% identification rate. This study developed an efficient molecular marker system for identifying apple and pear distant hybrid offspring based on InDel variation, providing a valuable tool for breeding new varieties of Rosaceae fruit trees.

A 5.2-kb insertion in the coding sequence of PavSCPL, a serine carboxypeptidase-like enhances fruit firmness in Prunus avium

Fruit firmness is an important trait in sweet cherry breeding because it directly positively influences fruit transportability, storage and shelf life. However, the underlying genes responsible and the molecular mechanisms that control fruit firmness remain unknown. In this study, we identified a candidate gene, PavSCPL, encoding a serine carboxypeptidase-like protein with natural allelic variation, that controls fruit firmness in sweet cherry using map-based cloning and functionally characterized PavSCPL during sweet cherry fruit softening. Genetic analysis revealed that fruit firmness in the 'Rainier' × 'Summit' F1 population was controlled by a single dominant gene. Bulked segregant analysis combined with fine mapping narrowed the candidate gene to a 473-kb region (7418778-7 891 914 bp) on chromosome 6 which included 72 genes. The candidate gene PavSCPL, and a null allele harbouring a 5244-bp insertion in the second exon that completely inactivated PavSCPL expression and resulted in the extra-hard-flesh phenotype, were identified by RNA-sequencing analysis and gene cloning. Quantitative RT-PCR analysis revealed that the PavSCPL expression level was increased with fruit softening. Virus-induced gene silencing of PavSCPL enhanced fruit firmness and suppressed the activities of certain pectin-degrading enzymes in the fruit. In addition, we developed functional molecular markers for PavSCPL and the Pavscpl5.2-k allele that co-segregated with the fruit firmness trait. Overall, this research identified a crucial functional gene for fruit firmness. The results provide insights into the genetic control and molecular mechanism of the fruit firmness trait and present useful molecular markers for molecular-assisted breeding for fruit firmness in sweet cherry.

Genome-Wide Association Mapping of Processing Quality Traits in Common Wheat (Triticum aestivum L.)

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.

Genome-wide association mapping in elite winter wheat breeding for yield improvement

Increased grain yield (GY) is the primary breeding target of wheat breeders. We performed the genome-wide association study (GWAS) on 168 elite winter wheat lines from an ongoing breeding program to identify the main determinants of grain yield. Sequencing of Diversity Array Technology fragments (DArTseq) resulted in 19,350 single-nucleotide polymorphism (SNP) and presence-absence variation (PAV) markers. We identified 15 main genomic regions located in ten wheat chromosomes (1B, 2B, 2D, 3A, 3D, 5A, 5B, 6A, 6B, and 7B) that explained from 7.9 to 20.3% of the variation in grain yield and 13.3% of the yield stability. Loci identified in the reduced genepool are important for wheat improvement using marker-assisted selection. We found marker-trait associations between three genes involved in starch biosynthesis and grain yield. Two starch synthase genes (TraesCS2B03G1238800 and TraesCS2D03G1048800) and a sucrose synthase gene (TraesCS3D03G0024300) were found in regions of QGy.rut-2B.2, QGy.rut-2D.1, and QGy.rut-3D, respectively. These loci and other significantly associated SNP markers found in this study can be used for pyramiding favorable alleles in high-yielding varieties or to improve the accuracy of prediction in genomic selection.

The Detection of Yr Genes in Xinjiang Wheat Cultivars Using Different Molecular Markers

Wheat stripe rust is a fungal disease caused by Puccinia striiformis f. sp. Tritici (Pst). It significantly impacts wheat yields in Xinjiang, China. Breeding and promoting disease-resistant cultivars carrying disease-resistance genes remains the most cost-effective strategy with which to control the disease. In this study, 17 molecular markers were used to identify Yr5, Yr9, Yr10, Yr15, Yr17, Yr18, Yr26, Yr41, Yr44, and Yr50 in 82 wheat cultivars from Xinjiang. According to the differences in SNP loci, the KASP markers for Yr30, Yr52, Yr78, Yr80, and Yr81 were designed and detected in the same set of 82 wheat cultivars. The results showed that there was a diverse distribution of Yr genes across all wheat cultivars in Xinjiang, and the detection rates of Yr5, Yr15, Yr17, Yr26, Yr41, and Yr50 were the highest, ranging from 74.39% to 98.78%. In addition, Yr5 and Yr15 were prevalent in spring wheat cultivars, with detection rates of 100% and 97.56%, respectively. A substantial 85.37% of wheat cultivars carried at least six or more different combinations of Yr genes. The cultivar Xindong No.15 exhibited the remarkable presence of 11 targeted Yr genes. The pedigree analysis results showed that 33.33% of Xinjiang wheat cultivars shared similar parentage, potentially leading to a loss of resistance against Pst. The results clarified the Yr gene distribution of the Xinjiang wheat cultivars and screened out varieties with a high resistance against Pst.

Biochemical and phenological characterization of diverse wheats and their association with drought tolerance genes

Drought is one of the most important wheat production limiting factor, and can lead to severe yield losses. This study was designed to examine the effect of drought stress on wheat physiology and morphology under three different field capacities (FC) viz. 80% (control), 50% (moderate) and 30% (severe drought stress) in a diverse collection of wheat germplasm including cultivars, landraces, synthetic hexaploid and their derivatives. Traits like grain weight, thousand grain weight and biomass were reduced by 38.23%, 18.91% and 26.47% respectively at 30% FC, whereas the reduction rate for these traits at 50% FC were 19.57%, 8.88% and 18.68%. In principal component analysis (PCA), the first two components PC1 and PC2 accounted for 58.63% of the total variation and separated the cultivars and landraces from synthetic-based germplasm. Landraces showed wide range of phenotypic variations at 30% FC compared to synthetic-based germplasm and improved cultivars. However, least reduction in grain weight was observed in improved cultivars which indicated the progress in developing drought resilient cultivars. Allelic variations of the drought-related genes including TaSnRK2.9-5A, TaLTPs-11, TaLTPs-12, TaSAP-7B-, TaPPH-13, Dreb-B1 and 1fehw3 were significantly associated with the phenological traits under drought stress in all 91 wheats including 40 landraces, 9 varieties, 34 synthetic hexaploids and 8 synthetic derivatives. The favorable haplotypes of 1fehw3, Dreb-B1, TaLTPs-11 and TaLTPs-12 increased grain weight, and biomass. Our results iterated the fact that landraces could be promising source to deploy drought adaptability in wheat breeding. The study further identified drought tolerant wheat genetic resources across various backgrounds and identified favourable haplotypes of water-saving genes which should be considered to develop drought tolerant varieties.

Wheat NAC-A18 regulates grain starch and storage proteins synthesis and affects grain weight

KEY MESSAGE

Wheat NAC-A18 regulates both starch and storage protein synthesis in the grain, and a haplotype with positive effects on grain weight showed increased frequency during wheat breeding in China. Starch and seed storage protein (SSP) directly affect the processing quality of wheat grain. The synthesis of starch and SSP are also regulated at the transcriptional level. However, only a few starch and SSP regulators have been identified in wheat. In this study, we discovered a NAC transcription factor, designated as NAC-A18, which acts as a regulator of both starch and SSP synthesis. NAC-A18, is predominately expressed in wheat developing grains, encodes a transcription factor localized in the nucleus, with both activation and repression domains. Ectopic expression of wheat NAC-A18 in rice significantly decreased starch accumulation and increased SSP accumulation and grain size and weight. Dual-luciferase reporter assays indicated that NAC-A18 could reduce the expression of TaGBSSI-A1 and TaGBSSI-A2, and enhance the expression of TaLMW-D6 and TaLMW-D1. A yeast one hybrid assay demonstrated that NAC-A18 bound directly to the cis-element "ACGCAA" in the promoters of TaLMW-D6 and TaLMW-D1. Further analysis indicated that two haplotypes were formed at NAC-A18, and that NAC-A18_h1 was a favorable haplotype correlated with higher thousand grain weight. Based on limited population data, NAC-A18_h1 underwent positive selection during Chinese wheat breeding. Our study demonstrates that wheat NAC-A18 regulates starch and SSP accumulation and grain size. A molecular marker was developed for the favorable allele for breeding applications.

Wheat end-use quality: State of art, genetics, genomics-assisted improvement, future challenges, and opportunities

Wheat is the most important source of food, feed, and nutrition for humans and livestock around the world. The expanding population has increasing demands for various wheat products with different quality attributes requiring the development of wheat cultivars that fulfills specific demands of end-users including millers and bakers in the international market. Therefore, wheat breeding programs continually strive to meet these quality standards by screening their improved breeding lines every year. However, the direct measurement of various end-use quality traits such as milling and baking qualities requires a large quantity of grain, traits-specific expensive instruments, time, and an expert workforce which limits the screening process. With the advancement of sequencing technologies, the study of the entire plant genome is possible, and genetic mapping techniques such as quantitative trait locus mapping and genome-wide association studies have enabled researchers to identify loci/genes associated with various end-use quality traits in wheat. Modern breeding techniques such as marker-assisted selection and genomic selection allow the utilization of these genomic resources for the prediction of quality attributes with high accuracy and efficiency which speeds up crop improvement and cultivar development endeavors. In addition, the candidate gene approach through functional as well as comparative genomics has facilitated the translation of the genomic information from several crop species including wild relatives to wheat. This review discusses the various end-use quality traits of wheat, their genetic control mechanisms, the use of genetics and genomics approaches for their improvement, and future challenges and opportunities for wheat breeding.

TaGSNE, a WRKY transcription factor, overcomes the trade-off between grain size and grain number in common wheat and is associated with root development

Wheat is one of the world's major staple food crops, and breeding for improvement of grain yield is a priority under the scenarios of climate change and population growth. WRKY transcription factors are multifaceted regulators in plant growth, development, and responses to environmental stimuli. In this study, we identify the WRKY gene TaGSNE (Grain Size and Number Enhancer) in common wheat, and find that it has relatively high expression in leaves and roots, and is induced by multiple abiotic stresses. Eleven single-nucleotide polymorphisms were identified in TaGSNE, forming two haplotypes in multiple germplasm collections, named as TaGSNE-Hap-1 and TaGSNE-Hap-2. In a range of different environments, TaGSNE-Hap-2 was significantly associated with increases in thousand-grain weight (TGW; 3.0%) and spikelet number per spike (4.1%), as well as with deeper roots (10.1%) and increased root dry weight (8.3%) at the mid-grain-filling stage, and these were confirmed in backcross introgression populations. Furthermore, transgenic rice lines overexpressing TaGSNE had larger panicles, more grains, increased grain size, and increased grain yield relative to the wild-type control. Analysis of geographic and temporal distributions revealed that TaGSNE-Hap-2 is positively selected in China and Pakistan, and TaGSNE-Hap-1 in Europe. Our findings demonstrate that TaGSNE overcomes the trade-off between TGW/grain size and grain number, leading us to conclude that these elite haplotypes and their functional markers could be utilized in marker-assisted selection for breeding high-yielding varieties.

Genetic basis analysis of key Loci in 23 Yannong series wheat cultivars/lines

Fungal diseases, drought, pre-harvest sprouting (PHS) and other biotic and abiotic stresses have seriously affected the quality and yield in wheat production. Identifying related genes/loci in released cultivars/lines can provide reference information and theoretical basis for wheat improvement. Yannong series wheat cultivars/lines have distinctive characteristics in wheat cultivars and play an important role in genetic improvement and production of Chinese wheat production system. To dissect their genetic basis of the stress-resistant traits, in this study, 23 representative Yannong series wheat cultivars/lines were tested by 58 molecular markers for 40 genes related to adaptability, disease resistance and stress tolerance to clarify the genetic composition of the key loci. The results showed that most of the tested wheat accessions carried dwarfing genes RhtB1b/RhtD1b/Rht8 and recessive vernalization genes vrn-A1/vrn-B1/vrn-D1/vrn-B3. It was also consistent with the phenotypic traits of tested Yannong series wheat which were dwarf and winter or semi winter wheat. In addition, the overall level of seedling powdery mildew resistance in 23 Yannong wheat cultivars/lines was moderate or inadequate. Eleven accessions carried none of the tested Pm genes and twelve accessions carried Pm2, Pm6, Pm42 and Pm52 singly or in combination. Then, 23 wheat cultivars/lines were also tested by 17 diagnostic markers for 14 Yr genes. The results showed that 16 wheat cultivars/lines were likely to carry one or more of tested Yr genes, whereas Yannong 15, Yannong 17, Yannong 23, Yannong 24, Yannong 377, Yannong 572 and Yannong 999 carried none of the tested Yr genes. Moreover, in our study, nine markers for four genes related to drought tolerance and PHS were used to evaluate the stress tolerance of the 23 wheat cultivars/lines. The results indicated that all 23 wheat cultivars/lines carried drought resistance genes Ta-Dreb1/TaCRT-D, indicating that they had the drought resistance to the extent. Except for Yannong 30, Yannong 377, Yannong 390, Yannong 745 and Yannong 1766, other wheat cultivars/lines carried one to three elite PHS-resistant alleles Vp-1Bc/Vp-1Bf/TaAFP-1Bb.

Identification of QTLs for wheat heading time across multiple-environments

KEY MESSAGE

The genetic response to changing climatic factors selects consistent across the tested environments and location-specific thermo-sensitive and photoperiod susceptible alleles in lower and higher altitudes, respectively, for starting flowering in winter wheat. Wheat breeders select heading date to match the most favorable conditions for their target environments and this is favored by the extensive genetic variation for this trait that has the potential to be further explored. In this study, we used a germplasm with broad geographic distribution and tested it in multi-location field trials across Germany over three years. The genotypic response to the variation in the climatic parameters depending on location and year uncovered the effect of photoperiod and spring temperatures in accelerating heading date in higher and lower latitudes, respectively. Spring temperature dominates other factors in inducing heading, whereas the higher amount of solar radiation delays it. A genome-wide scan of marker-trait associations with heading date detected two QTL: an adapted allele at locus TaHd102 on chromosome 5A that has a consistent effect on HD in German cultivars in multiple environments and a non-adapted allele at locus TaHd044 on chromosome 3A that accelerates flowering by 5.6 days. TaHd102 and TaHd044 explain 13.8% and 33% of the genetic variance, respectively. The interplay of the climatic variables led to the detection of environment specific association responding to temperature in lower latitudes and photoperiod in higher ones. Another locus TaHd098 on chromosome 5A showed epistatic interactions with 15 known regulators of flowering time when non-adapted cultivars from outside Germany were included in the analysis.

Trade-offs in the genetic control of functional and nutritional quality traits in UK winter wheat

A complex network of trade-offs exists between wheat quality and nutritional traits. We investigated the correlated relationships among several milling and baking traits as well as mineral density in refined white and whole grain flour. Our aim was to determine their pleiotropic genetic control in a multi-parent population over two trial years with direct application to practical breeding. Co-location of major quantitative trait loci (QTL) and principal component based multi-trait QTL mapping increased the power to detect QTL and revealed pleiotropic effects explaining many complementary and antagonistic trait relationships. High molecular weight glutenin subunit genes explained much of the heritable variation in important dough rheology traits, although additional QTL were detected. Several QTL, including one linked to the TaGW2 gene, controlled grain size and increased flour extraction rate. The semi-dwarf Rht-D1b allele had a positive effect on Hagberg falling number, but reduced grain size, specific weight, grain protein content and flour water absorption. Mineral nutrient concentrations were lower in Rht-D1b lines for many elements, in wholemeal and white flour, but potassium concentration was higher in Rht-D1b lines. The presence of awns increased calcium content without decreasing extraction rate, despite the negative correlation between these traits. QTL were also found that affect the relative concentrations of key mineral nutrients compared to phosphorus which may help increase bioavailability without associated anti-nutritional effects of phytic acid. Taken together these results demonstrate the potential for marker-based selection to optimise trait trade-offs and enhance wheat nutritional value by considering pleiotropic genetic effects across multiple traits.

Identification of Resistant Germplasm and Detection of Genes for Resistance to Powdery Mildew and Leaf Rust from 2,978 Wheat Accessions

Powdery mildew and leaf rust, caused by Blumeria graminis f. sp. tritici and Puccinia triticina, respectively, are widespread diseases of wheat worldwide. The use of resistant cultivars is considered the most economical, environment-friendly, and effective method to control these diseases. In the present study, a collection of 2,978 wheat accessions consisting of 1,394 advanced breeding lines, 1,078 Chinese cultivars, 291 introduced cultivars, 132 lines containing alien chromosomes, and 83 landraces was tested for reactions to powdery mildew and leaf rust. The results indicated that 659 wheat accessions (22.1%) were highly resistant to a widely prevalent B. graminis f. sp. tritici isolate, E09, at the seedling stage, and 390 were consistently resistant to the mixture of B. graminis f. sp. tritici isolates at the adult plant stage. Meanwhile, 63 accessions (2.1%) were highly resistant to leaf rust at the adult plant stage, of which 54 were resistant to a predominant and highly virulent P. triticina race, THTT, at the seedling stage. Notably, 17 accessions were resistant to both powdery mildew and leaf rust. To detect known genes for resistance to powdery mildew and leaf rust, these accessions were tested with gene-specific or tightly linked markers for seven powdery mildew genes (Pm genes; Pm2, Pm4, Pm5, Pm6, Pm8, Pm21, and Pm24) and 10 Lr genes (Lr1, Lr9, Lr10, Lr19, Lr20, Lr24, Lr26, Lr34, Lr37, and Lr46). Of the 659 powdery mildew-resistant accessions, 328 might carry single Pm genes and 191 carry combined Pm genes. Pm2 was detected at the highest frequency of 59.6%, followed by Pm8, Pm6, Pm21, Pm4, and Pm5, whereas Pm24 was not detected. In addition, 139 accessions might contain unknown Pm genes different from those tested in this study. In the 63 accessions resistant to leaf rust, four leaf rust genes (Lr genes; Lr1, Lr10, Lr26, and Lr34) were detected in 41 accessions singly or in combination, whereas six genes (Lr9, Lr19, Lr20, Lr24, Lr37, and Lr46) were not detected. Twenty-two accessions might contain unknown Lr genes different from those tested in this study. This study not only provided important information for rationally distributing resistance genes in wheat breeding programs, but also identified resistant germplasm that might have novel genes to enrich the diversity of resistance sources.

Developing functional markers for vitamin E biosynthesis in oil palm

Vitamin E is essential for human health and plays positive roles in anti-oxidation. Previously, we detected large variation in vitamin E content among 161 oil palm accessions. In this study, twenty oil palm accessions with distinct variation in vitamin E contents (171.30 to 1 258.50 ppm) were selected for genetic variation analysis and developing functional markers associated with vitamin E contents. Thirty-seven homologous genes in oil palm belonging to vitamin E biosynthesis pathway were identified via BLASTP analysis, the lengths of which ranged from 426 to 25 717 bp (average 7 089 bp). Multiplex PCR sequencing for the 37 genes found 1 703 SNPs and 85 indels among the 20 oil palm accessions, with 226 SNPs locating in the coding regions. Clustering analysis for these polymorphic loci showed that the 20 oil palm accessions could be divided into five groups. Among these groups, group I included eight oil palm accessions whose vitamin E content (mean value: 893.50 ppm) was far higher than other groups (mean value 256.29 to 532.94 ppm). Correlation analysis between the markers and vitamin E traits showed that 134 SNP and 7 indel markers were significantly (p < 0.05) related with total vitamin E content. Among these functional markers, the indel EgTMT-1-24 was highly correlated with variation in vitamin E content, especially tocotrienol content. Our study identified a number of candidate function associated markers and provided clues for further research into molecular breeding for high vitamin E content oil palm.

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.

Recent advancements in molecular marker-assisted selection and applications in plant breeding programmes

Background

DNA markers improved the productivity and accuracy of classical plant breeding by means of marker-assisted selection (MAS). The enormous number of quantitative trait loci (QTLs) mapping read for different plant species have given a plenitude of molecular marker-gene associations.

Main body of the abstract

In this review, we have discussed the positive aspects of molecular marker-assisted selection and its precise applications in plant breeding programmes. Molecular marker-assisted selection has considerably shortened the time for new crop varieties to be brought to the market. To explore the information about DNA markers, many reviews have been published in the last few decades; all these reviews were intended by plant breeders to obtain information on molecular genetics. In this review, we intended to be a synopsis of recent developments of DNA markers and their application in plant breeding programmes and devoted to early breeders with little or no knowledge about the DNA markers. The progress made in molecular plant breeding, plant genetics, genomics selection, and editing of genome contributed to the comprehensive understanding of DNA markers and provides several proofs on the genetic diversity available in crop plants and greatly complemented plant breeding devices.

Short conclusion

MAS has revolutionized the process of plant breeding with acceleration and accuracy, which is continuously empowering plant breeders around the world.

Association Analysis Revealed That TaPYL4 Genes Are Linked to Plant Growth Related Traits in Multiple Environment

Abscisic acid (ABA), one of phytohormones, plays an important regulatory role in plant growth and development. ABA receptor PYL4 (pyrabactin resistance 1-like 4) was previously detected to be involved in plant response to a variety of stresses. TaPYL4 overexpression could enhance wheat (Triticum aestivum) drought resistance. In order to further investigate TaPYL4's role in regulating development of other major agronomic traits in wheat, genes of TaPYL4-2A, TaPYL4-2B, and TaPYL4-2D were cloned from wheat, respectively. Polymorphism analysis on TaPYL4 sequences revealed that encoding regions of the three genes were highly conserved, without any SNP (single nucleotide polymorphism) presence. However, nine SNPs and four SNPs were identified in the promoter regions of TaPYL4-2A and TaPYL4-2B, respectively. Functional molecular markers were developed based on these polymorphisms, which were then used to scan a natural population of 323 common wheat accessions for correlation analysis between genotype and the target phenotypic traits. Both TaPYL4-2A and TaPYL4-2B markers were significantly correlated with plant growth-related traits under multiple environments (well-watered, drought and heat stress treatments). The additive effects of TaPYL4-2A and TaPYL4-2B were verified by the combinational haplotype (Hap-AB1∼Hap-AB4) effects determined from field data. Cis-acting elements were analyzed in the promoters of TaPYL4-2A and TaPYL4-2B, showing that a TGA-element bound by ARFs (auxin response factors) existed only in Hap-2A-1 of TaPYL4-2A. Gene expression assays indicated that TaPYL4-2A was constitutively expressed in various tissues, with higher expression in Hap-2A-1 genotypes than in Hap-2A-2 materials. Notably, TaARF4 could act as TaPYL4-2A transcription activator in Hap-2A-1 materials, but not in Hap-2A-2 genotypes. Analysis of geographic distribution and temporal frequency of haplotypes indicated that Hap-AB1 was positively selected in wheat breeding in China. Therefore, TaPYL4-2A and TaPYL4-2B could be a valuable target gene in wheat genetic improvement to develop the ideal plant architecture.

Identification of Candidate Gene-Based Markers for Girth Growth in Rubber Trees

Girth growth is an important factor in both latex and timber production of the rubber tree. In this study, we performed candidate gene association mapping for girth growth in rubber trees using intron length polymorphism markers (ILP) in identifying the candidate genes responsible for girth growth. The COBL064_1 marker developed from the candidate gene (COBL4) regulating cellulose deposition and oriented cell expansion in the plant cell wall showed the strongest association with girth growth across two seasons in the Amazonian population and was validated in the breeding lines. We then applied single molecule real-time (SMRT) circular consensus sequencing (CCS) to analyze a wider gene region of the COBL4 to pinpoint the single nucleotide polymorphism (SNP) that best explains the association with the traits. A SNP in the 3’ UTR showing linkage disequilibrium with the COBL064_1 most associated with girth growth. This study showed that the cost-effective method of ILP gene-based markers can assist in identification of SNPs in the candidate gene associated with girth growth. The SNP markers identified in this study added useful markers for the improvement of girth growth in rubber tree breeding programs.

Identification of Single Nucleotide Polymorphism in TaSBEIII and Development of KASP Marker Associated With Grain Weight in Wheat

Manipulation of genes involved in starch synthesis could significantly affect wheat grain weight and yield. The starch-branching enzyme (SBE) catalyzes the formation of branch points by cleaving the α-1,4 linkage in polyglucans and reattaching the chain via an α-1,6 linkage. Three types of SBE isoforms (SBEI, SBEII, and SBEIII) exist in higher plants, with the number of SBE isoforms being species-specific. In this study, the coding sequence of the wheat TaSBEIII gene was amplified. After the multiple sequence alignment of TaSBEIII genome from 20 accessions in a wheat diversity panel, one SNP was observed in TaSBEIII-A, which formed the allelic marker allele-T. Based on this SNP at 294 bp (C/T), a KASP molecular marker was developed to distinguish allelic variation among the wheat genotypes for thousand grain weight (TGW). The results were validated using 262 accessions of mini core collection (MCC) from China, 153 from Pakistan, 53 from CIMMYT, and 17 diploid and 18 tetraploid genotypes. Association analysis between TaSBEIII-A allelic variation and agronomic traits found that TaSBEIII-A was associated with TGW in mini core collection of China (MCC). The accessions possessing Allele-T had higher TGW than those possessing Allele-C; thus, Allele-T was a favorable allelic variation. By analyzing the frequency of the favorable allelic variation Allele-T in MCC, it increased from pre-1950 (25%) to the 1960s (45%) and increased continuously from 1960 to 1990 (80%). The results suggested that the KASP markers can be utilized in grain weight improvement, which ultimately improves wheat yield by marker-assisted selection in wheat breeding. The favorable allelic variation allele-T should be valuable in enhancing grain yield by improving the source and sink simultaneously. Furthermore, the newly developed KASP marker validated in different genetic backgrounds could be integrated into a breeding kit for screening high TGW wheat.

Kibr G. Effect of blending ratio of wheat, orange fleshed sweet potato and haricot bean flour on proximate compositions, β-carotene, physicochemical properties and sensory acceptability of biscuits'

Background: Protein-energy malnutrition and vitamin A deficiency (VAD) are the most important public health issues, and a food-based strategy is crucial to combat those health problems among the vulnerable group of people. Methods: Composite biscuits were made with 100:0:0, 90:5:5, 80:10:10, 70:15:15, 60:20:20, and 50:25:25 percent wheat, haricot bean, and orange-fleshed sweet potato (OFSP) flours.Standard methods were used to evaluate the proximate compositions, β-carotene, physical properties, functional properties, and sensory acceptability. A one-way analysis of variance model was used to statistically evaluate the data using the statistical analysis system software package, version 9.0 standard methods. Results: The results showed that partially replacing wheat with haricot beans and OFSP increased the β-carotene and proximate compositions significantly. When wheat was replaced with haricot beans and OFSP, the physical characteristics of the biscuits did not vary significantly from those of biscuits made entirely of wheat flour. Sensory acceptability (appearance, color, flavor, taste and overall acceptability) was higher in the composite biscuits with up to 40% wheat substitution than in the 100% wheat flour biscuits. Conclusion: Based on the findings of this report, replacing wheat with OFSP and haricot beans in biscuit formulation appears to be promising in improving nutritional quality, sensory acceptability, and beta carotene. It is proposed that these products can mitigate food insecurity and deficiency of vitamin A.

Development and Exploitation of KASP Assays for Genes Underpinning Drought Tolerance Among Wheat Cultivars From Pakistan

High-throughput genotyping for functional markers offers an excellent opportunity to effectively practice marker-assisted selection (MAS) while breeding cultivars. We developed kompetitive allele-specific PCR (KASP) assays for genes conferring drought tolerance in common wheat (Triticum aestivum L.). In total, 11 KASP assays developed in this study and five already reported assays were used for their application in wheat breeding. We investigated alleles at 16 loci associated with drought tolerance among 153 Pakistani hexaploid wheat cultivars released during 1953-2016; 28 diploid wheat accessions (16 for AA and 12 for BB) and 19 tetraploid wheat (AABB) were used to study the evolutionary history of the studied genes. Superior allelic variations of the studied genes were significantly associated with higher grain yield. Favored haplotypes of TaSnRK2.3-1A, TaSnRK2.3-1B, TaSnRK2.9-5A, TaSAP-7B, and TaLTPs-1A predominated in Pakistani wheat germplasm indicating unconscious pyramiding and selection pressure on favorable haplotypes during selection breeding. TaSnRK2.8-5A, TaDreb-B1, 1-feh w3, TaPPH-7A, TaMOC-7A, and TaPARG-2A had moderate to low frequencies of favorable haplotype among Pakistani wheat germplasm pointing toward introgression of favorable haplotypes by deploying functional markers in marker-assisted breeding. The KASP assays were compared with gel-based markers for reliability and phenotypically validated among 62 Pakistani wheat cultivars. Association analyses showed that the favorable allelic variations were significantly associated with grain yield-contributing traits. The developed molecular marker toolkit of the genes can be instrumental for the wheat breeding in Pakistan.

Wheat omics: Classical breeding to new breeding technologies

Wheat is an important cereal crop, and its significance is more due to compete for dietary products in the world. Many constraints facing by the wheat crop due to environmental hazardous, biotic, abiotic stress and heavy matters factors, as a result, decrease the yield. Understanding the molecular mechanism related to these factors is significant to figure out genes regulate under specific conditions. Classical breeding using hybridization has been used to increase the yield but not prospered at the desired level. With the development of newly emerging technologies in biological sciences i.e., marker assisted breeding (MAB), QTLs mapping, mutation breeding, proteomics, metabolomics, next-generation sequencing (NGS), RNA_sequencing, transcriptomics, differential expression genes (DEGs), computational resources and genome editing techniques i.e. (CRISPR cas9; Cas13) advances in the field of omics. Application of new breeding technologies develops huge data; considerable development is needed in bioinformatics science to interpret the data. However, combined omics application to address physiological questions linked with genetics is still a challenge. Moreover, viroid discovery opens the new direction for research, economics, and target specification. Comparative genomics important to figure gene of interest processes are further discussed about considering the identification of genes, genomic loci, and biochemical pathways linked with stress resilience in wheat. Furthermore, this review extensively discussed the omics approaches and their effective use. Integrated plant omics technologies have been used viroid genomes associated with CRISPR and CRISPR-associated Cas13a proteins system used for engineering of viroid interference along with high-performance multidimensional phenotyping as a significant limiting factor for increasing stress resistance in wheat.

Functional gene assessment of bread wheat: breeding implications in Ningxia Province

BACKGROUND

The overall genetic distribution and divergence of cloned genes among bread wheat varieties that have occurred during the breeding process over the past few decades in Ningxia Province, China, are poorly understood. Here, we report the genetic diversities of 44 important genes related to grain yield, quality, adaptation and resistance in 121 Ningxia and 86 introduced wheat cultivars and advanced lines.

RESULTS

The population structure indicated characteristics of genetic components of Ningxia wheat, including landraces of particular genetic resources, introduced varieties with rich genetic diversities and modern cultivars in different periods. Analysis of allele frequencies showed that the dwarfing alleles Rht-B1b at Rht-B1 and Rht-D1b at Rht-D1, 1BL/1RS translocation, Hap-1 at GW2-6B and Hap-H at Sus2-2B are very frequently present in modern Ningxia cultivars and in introduced varieties from other regions but absent in landraces. This indicates that the introduced wheat germplasm with numerous beneficial genes is vital for broadening the genetic diversity of Ningxia wheat varieties. Large population differentiation between modern cultivars and landraces has occurred in adaptation genes. Founder parents carry excellent allele combinations of important genes, with a higher number of favorable alleles than modern cultivars. Gene flow analysis showed that six founder parents have greatly contributed to breeding improvement in Ningxia Province, particularly Zhou 8425B, for yield-related genes.

CONCLUSIONS

Varieties introduced from other regions with rich genetic diversity and landraces with well-adapted genetic resources have been applied to improve modern cultivars. Founder parents, particularly Zhou 8425B, for yield-related genes have contributed greatly to wheat breeding improvement in Ningxia Province. These findings will greatly benefit bread wheat breeding in Ningxia Province as well as other areas with similar ecological environments.

How the pan-genome is changing crop genomics and improvement

Crop genomics has seen dramatic advances in recent years due to improvements in sequencing technology, assembly methods, and computational resources. These advances have led to the development of new tools to facilitate crop improvement. The study of structural variation within species and the characterization of the pan-genome has revealed extensive genome content variation among individuals within a species that is paradigm shifting to crop genomics and improvement. Here, we review advances in crop genomics and how utilization of these tools is shifting in light of pan-genomes that are becoming available for many crop species.

How the pan-genome is changing crop genomics and improvement

Crop genomics has seen dramatic advances in recent years due to improvements in sequencing technology, assembly methods, and computational resources. These advances have led to the development of new tools to facilitate crop improvement. The study of structural variation within species and the characterization of the pan-genome has revealed extensive genome content variation among individuals within a species that is paradigm shifting to crop genomics and improvement. Here, we review advances in crop genomics and how utilization of these tools is shifting in light of pan-genomes that are becoming available for many crop species.

Transcription Factor TaWRKY51 Is a Positive Regulator in Root Architecture and Grain Yield Contributing Traits

Wheat is one of the staple food crops. The utilization of elite genetic resources to develop resource-efficient wheat varieties is an effective approach to deal with the challenges of climate change and population growth. WRKY transcription factors (TFs) are multifaceted regulators of plant growth and development and response to environmental stress. The previous studies have shown that TaWRKY51 positively regulates the development of lateral roots, while its roles in agronomic trait development are not clear, and there is no functional marker for molecular breeding. To bridge the gap, we cloned the three members of TaWRKY51 and found they were highly expressed in the roots and flag leaves at the flowering stage and were induced by the multiple abiotic stresses and phytohormones. The highest expression level was observed in TaWRKY51-2D, followed by TaWRKY51-2A and -2B. The two haplotypes/alleles for each member were identified in the natural populations, and functional markers were developed accordingly. The association assays revealed that Hap-2A-I was an elite haplotype for the large spike, Hap-2B-II and allele-G were favorable haplotypes/alleles for long root. However, only Hap-2A-I was selected for wheat breeding in China. The results of transgenic experiments showed that the rice lines overexpressing TaWRKY51 had large panicle, high thousand-grain-weight, and more crown and lateral roots, which further confirmed the results of association analysis. In short, TaWRKY51 is a positive regulator of the root architecture and grain yield (GY) contributing traits. The elite gene resources and functional markers may be utilized in the marker-assisted selection for high-yield breeding in wheat.

Ecological genomics of Chinese wheat improvement: implications in breeding for adaptation

BACKGROUND

China has diverse wheat varieties that adapt to very different environments divided into ten agro-ecological zones. A better understanding of genomic differences and patterns of selection among agro-ecological zones could provide useful information in selection of specific adaptive traits in breeding.

RESULTS

We genotyped 438 wheat accessions from ten zones with kompetitive allele specific PCR (KASP) markers specific to 47 cloned genes for grain yield, quality, adaptation and stress resistance. Phylogenetic trees and principle component analysis revealed clear differences in winter and spring growth habits. Nucleotide diversity (π) and π ratio (π_CL/π_MCC) suggested that genetic diversity had increased during breeding, and that Chinese landraces (CL) from Zones I-V contributed little to modern Chinese cultivars (MCC). π ratio and Fst identified 24 KASP markers with 53 strong selection signals specific to Zones I (9 signals), II (12), III (5), IV (5), V (6), and VI (6). Genes with clear genetic differentiation and strong response to selection in at least three zones were leaf rust resistance gene Lr34 (I, II, III and IV), photoperiod sensitivity gene Ppd-D1 (I, II, III, IV and V), vernalization gene Vrn-B1 (V, VII, VIII and X), quality-related gene Glu-B1 (I, II and III) and yield-related genes Sus1-7B (I, II, III, IV and IX), Sus2-2A (I, II, III., IV and VI) and GW2-6B (II, V and VI).

CONCLUSIONS

This study examined selection of multiple genes in each zone, traced the distribution of important genetic variations and provided useful information for ecological genomics and enlightening future breeding goals for different agro-ecological zones.

The MYB transcription factor TaPHR3-A1 is involved in phosphate signaling and governs yield-related traits in bread wheat

Improved inorganic phosphate (Pi) use efficiency in crops will be important for sustainable agriculture. Exploring molecular mechanisms that regulate Pi uptake could provide useful information for breeding wheat with improved Pi use efficiency. Here, a TaPHR3-A1 (Gene ID: TraesCS7A02G415800) ortholog of rice OsPHR3 that functions in transcriptional regulation of Pi signaling was cloned from wheat chromosome 7A. Ectopic expression of TaPHR3-A1 in Arabidopsis and rice produced enhanced vegetative growth and more seeds. Overexpression in transgenic rice led to increased biomass, grain number, and primary panicle branching by 61.23, 42.12, and 36.34% compared with the wild type. Transgenic wheat lines with down-regulation of TaPHR3-A1 exhibited retarded growth and root hair development at the seedling stage, and showed yield-related effects at the adult stage when grown in both low- and sufficient Pi conditions, indicating that TaPHR3-A1 positively regulated tolerance to low Pi. Introgression lines further confirmed the effect of TaPHR3-A1 in improving grain number. The Chinese wheat mini core collection and a recombinant inbred line analysis demonstrated that the favorable allele TaPHR3-A1-A associated with higher grain number was positively selected in breeding. A TaPHR3-A1-derived cleaved amplified polymorphic sequence marker effectively identified haplotype TaPHR3-A1-A. Our results suggested that TaPHR3-A1 was a functional regulatory factor for Pi uptake and provided useful information for marker-assisted selection for high yield in wheat.

Grain Size Selection Using Novel Functional Markers Targeting 14 Genes in Rice

BACKGROUND

Grain size is an extremely important aspect of rice breeding, affecting both grain yield and quality traits. It is controlled by multiple genes and tracking these genes in breeding schemes should expedite selection of lines with superior grain yield and quality, thus it is essential to develop robust, efficient markers.

RESULT

In this study, 14 genes related to grain size (GW2, GS2, qLGY3, GS3, GL3.1, TGW3, GS5, GW5, GS6, TGW6, GW6a, GLW7, GL7 and GW8) were selected for functional marker development. Twenty-one PCR-gel-based markers were developed to genotype the candidate functional nucleotide polymorphisms (FNPs) of these genes, and all markers can effectively recognize the corresponding allele types. To test the allele effects of different FNPs, a global collection of rice cultivars including 257 accessions from the Rice Diversity Panel 1 was used for allele mining, and four grain-size-related traits were investigated at two planting locations. Three FNPs for GW2, GS2 and GL3.1 were genotyped as rare alleles only found in cultivars with notably large grains, and the allele contributions of the remaining FNPs were clarified in both the indica and japonica subspecies. Significant trait contributions were found for most of the FNPs, especially GS3, GW5 and GL7. Of note, GW5 could function as a key regulator to coordinate the performance of other grain size genes. The allele effects of several FNPs were also tested by QTL analysis using an F2 population, and GW5 was further identified as the major locus with the largest contribution to grain width and length to width ratio.

CONCLUSIONS

The functional markers are robust for genotyping different cultivars and may facilitate the rational design of grain size to achieve a balance between grain yield and quality in future rice breeding efforts.

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.

Functional Markers for Precision Plant Breeding

Advances in molecular biology including genomics, high-throughput sequencing, and genome editing enable increasingly faster and more precise cultivar development. Identifying genes and functional markers (FMs) that are highly associated with plant phenotypic variation is a grand challenge. Functional genomics approaches such as transcriptomics, targeting induced local lesions in genomes (TILLING), homologous recombinant (HR), association mapping, and allele mining are all strategies to identify FMs for breeding goals, such as agronomic traits and biotic and abiotic stress resistance. The advantage of FMs over other markers used in plant breeding is the close genomic association of an FM with a phenotype. Thereby, FMs may facilitate the direct selection of genes associated with phenotypic traits, which serves to increase selection efficiencies to develop varieties. Herein, we review the latest methods in FM development and how FMs are being used in precision breeding for agronomic and quality traits as well as in breeding for biotic and abiotic stress resistance using marker assisted selection (MAS) methods. In summary, this article describes the use of FMs in breeding for development of elite crop cultivars to enhance global food security goals.

Economical optimization of a breeding scheme by selective phenotyping of the calibration set in a multi-trait context: application to bread making quality

Trait-assisted genomic prediction approach is a way to improve genetic gain by cost unit, by reducing budget allocated to phenotyping or by increasing the program's size for the same budget. This study compares different strategies of genomic prediction to optimize resource allocation in breeding schemes by using information from cheaper correlated traits to predict a more expensive trait of interest. We used bread wheat baking score (BMS) calculated for French registration as a case study. To conduct this project, 398 lines from a public breeding program were genotyped and phenotyped for BMS and correlated traits in 11 locations in France between 2000 and 2016. Single-trait (ST), multi-trait (MT) and trait-assisted (TA) strategies were compared in terms of predictive ability and cost. In MT and TA strategies, information from dough strength (W), a cheaper trait correlated with BMS (r = 0.45), was evaluated in the training population or in both the training and the validation sets, respectively. TA models allowed to reduce the budget allocated to phenotyping by up to 65% while maintaining the predictive ability of BMS. TA models also improved the predictive ability of BMS compared to ST models for a fixed budget (maximum gain: + 0.14 in cross-validation and + 0.21 in forward prediction). We also demonstrated that the budget can be further reduced by approximately one fourth while maintaining the same predictive ability by reducing the number of phenotypic records to estimate BMS adjusted means. In addition, we showed that the choice of the lines to be phenotyped can be optimized to minimize cost or maximize predictive ability. To do so, we extended the mean of the generalized coefficient of determination (CD_mean) criterion to the multi-trait context (CD_multi).

The Wheat 660K SNP array demonstrates great potential for marker-assisted selection in polyploid wheat

The rapid development and application of molecular marker assays have facilitated genomic selection and genome-wide linkage and association studies in wheat breeding. Although PCR-based markers (e.g. simple sequence repeats and functional markers) and genotyping by sequencing have contributed greatly to gene discovery and marker-assisted selection, the release of a more accurate and complete bread wheat reference genome has resulted in the design of single-nucleotide polymorphism (SNP) arrays based on different densities or application targets. Here, we evaluated seven types of wheat SNP arrays in terms of their SNP number, distribution, density, associated genes, heterozygosity and application. The results suggested that the Wheat 660K SNP array contained the highest percentage (99.05%) of genome-specific SNPs with reliable physical positions. SNP density analysis indicated that the SNPs were almost evenly distributed across the whole genome. In addition, 229 266 SNPs in the Wheat 660K SNP array were located in 66 834 annotated gene or promoter intervals. The annotated genes revealed by the Wheat 660K SNP array almost covered all genes revealed by the Wheat 35K (97.44%), 55K (99.73%), 90K (86.9%) and 820K (85.3%) SNP arrays. Therefore, the Wheat 660K SNP array could act as a substitute for other 6 arrays and shows promise for a wide range of possible applications. In summary, the Wheat 660K SNP array is reliable and cost-effective and may be the best choice for targeted genotyping and marker-assisted selection in wheat genetic improvement.

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.

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.

QTL mapping for grain yield-related traits in bread wheat via SNP-based selective genotyping

We identified four chromosome regions harboring QTL for grain yield-related traits, and breeder-friendly KASP markers were developed and validated for marker-assisted selection. Identification of major stable quantitative trait loci (QTL) for grain yield-related traits is important for yield potential improvement in wheat breeding. In the present study, 266 recombinant inbred lines (RILs) derived from a cross between Zhongmai 871 (ZM871) and its sister line Zhongmai 895 (ZM895) were evaluated for thousand grain weight (TGW), grain length (GL), grain width (GW), and grain number per spike (GNS) in 10 environments and for grain filling rate in six environments. Sixty RILs, with 30 higher and 30 lower TGW, respectively, were genotyped using the wheat 660 K SNP array for preliminary QTL mapping. Four genetic regions on chromosomes 1AL, 2BS, 3AL, and 5B were identified to have a significant effect on TGW-related traits. A set of Kompetitive Allele Specific PCR markers were converted from the SNP markers on the above target chromosomes and used to genotype all 266 RILs. The mapping results confirmed the QTL named Qgw.caas-1AL, Qgl.caas-3AL, Qtgw.caas-5B, and Qgl.caas-5BS on the targeted chromosomes, explaining 5.0-20.6%, 5.7-15.7%, 5.5-17.3%, and 12.5-20.5% of the phenotypic variation for GW, GL, TGW, and GL, respectively. A novel major QTL for GNS on chromosome 5BS, explaining 5.2-15.2% of the phenotypic variation, was identified across eight environments. These QTL were further validated using BC₁F₄ populations derived from backcrosses ZM871/ZM895//ZM871 (121 lines) and ZM871/ZM895//ZM895 (175 lines) and 186 advanced breeding lines. Collectively, selective genotyping is a simple, economic, and effective approach for rapid QTL mapping and can be generally applied to genetic mapping studies for important agronomic traits.

SNP markers for early identification of high molecular weight glutenin subunits (HMW-GSs) in bread wheat

A set of eight SNP markers was developed to facilitate the early selection of HMW-GS alleles in breeding programmes. In bread wheat (Triticum aestivum), the high molecular weight glutenin subunits (HMW-GSs) are the most important determinants of technological quality. Known to be very diverse, HMW-GSs are encoded by the tightly linked genes Glu-1-1 and Glu-1-2. Alleles that improve the quality of dough have been identified. Up to now, sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) of grain proteins is the most widely used for their identification. To facilitate the early selection of HMW-GS alleles in breeding programmes, we developed DNA-based molecular markers. For each accession of a core collection (n = 364 lines) representative of worldwide bread wheat diversity, HMW-GSs were characterized by both genotyping and SDS-PAGE. Based on electrophoresis, we observed at least 8, 22 and 9 different alleles at the Glu-A1, Glu-B1 and Glu-D1 loci, respectively, including new variants. We designed a set of 17 single-nucleotide polymorphism (SNP) markers that were representative of the most frequent SDS-PAGE alleles at each locus. At Glu-A1 and Glu-D1, two and three marker-based haplotypes, respectively, captured the diversity of the SDS-PAGE alleles rather well. Discrepancies were found mainly for the Glu-B1 locus. However, statistical tests revealed that two markers at each Glu-B1 gene and their corresponding haplotypes were more significantly associated with the rheological properties of the dough than were the relevant SDS-PAGE alleles. To conclude, this study demonstrates that the SNP markers developed provide additional information on HMW-GS diversity. Two markers at Glu-A1, four at Glu-B1 and two at Glu-D1 constitute a useful toolbox for breeding wheat to improve end-use value.

Identification, Characterization, and Evaluation of Novel Stripe Rust-Resistant Wheat-Thinopyrum intermedium Chromosome Translocation Lines

Stripe rust is an important disease in wheat, and development of genetic resistance in cultivars is an effective approach to control the disease. Wild species of wheat, such as Thinopyrum intermedium, are an excellent gene source for wheat improvement. In this study, two stripe rust-resistant wheat-Th. intermedium chromosome translocation lines, CH4131 and CH4132, were characterized by cytogenetic and pathological methods. The introgressed chromosome fragment was tagged using amplified fragment-length polymorphism-derived sequence-characterized amplified region (SCAR) markers and intron targeting markers, indicating that CH4131 and CH4132 both possess a homologous group 3 chromatin of Th. intermedium. Genomic in situ hybridization results suggested that a very small Th. intermedium chromosome segment was translocated to the terminal region of wheat 1BS for both lines, forming a configuration of T3Ai-1BS.1BL. The two translocation lines were resistant to stripe rust, and the resistance gene, temporarily designated YrCH-1BS, was likely derived from Th. intermedium. The translocated chromosome fragments have no genetic linkage drag to agronomic performance. The grain quality indexes of these two translocations were higher than local wheat varieties. Therefore, CH4131 and CH4132 could be used as potential gene sources in wheat improvement programs. The SCAR markers are useful to select stripe rust resistance from Th. intermedium.

Identification of TaPPH-7A haplotypes and development of a molecular marker associated with important agronomic traits in common wheat

BACKGROUND

Premature senescence of flag leaf severely affects wheat yield and quality. Chlorophyll (Chl) degradation is the most obvious symptom during leaf senescence and catalyzed by a series of enzymes. Pheophytin pheophorbide hydrolase (Pheophytinase, PPH) gene encodes a Chl degradation hydrolase.

RESULTS

In this study, the coding, genomic and promoter sequences of wheat TaPPH-A gene were cloned. The corresponding lengths were 1467 bp, 4479 bp and 3666 bp, respectively. Sequence structure analysis showed that TaPPH-A contained five exons and four introns. After the multiple sequences alignment of TaPPH-A genome from 36 accessions in a wheat diversity panel, four SNPs and one 2-bp InDel were observed, which formed two haplotypes, TaPPH-7A-1 and TaPPH-7A-2. Based on the SNP at 1299 bp (A/G), a molecular marker TaPPH-7A-dCAPS was developed to distinguish allelic variation (A/G). Using the molecular markers, 13 SSR, and 116 SNP markers, a linkage map of chromosome 7A were integrated. TaPPH-A was mapped on the chromosome region flanked by Xwmc9 (0.94 cM) and AX-95634545 (1.04 cM) on 7A in a DH population. Association analysis between TaPPH-7A allelic variation and agronomic traits found that TaPPH-7A was associated with TGW in 11 of 12 environments and Chl content at grain-filling stage under drought stress using Population 1 consisted of 323 accessions. The accessions possessed TaPPH-7A-1 (A) had higher TGW and Chl content than those possessed TaPPH-7A-2 (G), thus TaPPH-7A-1 (A) was a favorable allelic variation. By analyzing the frequency of favorable allelic variation TaPPH-7A-1 (A) in Population 2 with 157 landraces and Population 3 with 348 modern cultivars, we found it increased from pre-1950 (0) to 1960s (54.5%), then maintained a relatively stable level about 56% from 1960s to 1990s.

CONCLUSION

These results suggested the favorable allelic variation TaPPH-7A-1 (A) should be valuable in enhancing grain yield by improving the source (chlorophyll content) and sink (the developing grain) simultaneously. Furthermore, the newly developed molecular marker TaPPH-7A-dCAPS could be integrated into a breeding kit of screening high TGW wheat for marker-assisted selection.

Insights into deployment of DNA markers in plant variety protection and registration

The efficiency of phenotype-based assessments of plant variety protection and registration could be improved by the integration of DNA-based testing. We review the current and proposed models in the era of next-generation breeding. The current plant variety protection system relies on morphological description of plant varieties. Distinctness, uniformity, and stability (DUS) assessments determine whether a new variety is distinguishable from common knowledge varieties and exhibits sufficient phenotypic uniformity and stability during two independent growing cycles. However, DUS assessment can be costly, time-consuming and often restricted to a relatively small number of traits that can be influenced by environmental conditions. This calls for the adoption of a DNA-based system which is endorsed by the International Union for the Protection of New Varieties of Plants (UPOV). This could enable examiners to deploy trait-specific DNA markers in DUS testing as well as using such genetic markers to manage reference collections. Within UPOV's system, breeders can freely use protected varieties in breeding programs. However, breeders of protected varieties may seek sharing in ownership of essentially derived varieties once it is proven that they, with the exception of a few distinctive DUS trait(s), conform to parental varieties in essential characteristics. As well as their complementary role in DUS testing, DNA markers have been known as a good replacement of morphological traits in defining boundaries between independently and essentially derived varieties. With the advent of new breeding technologies that allow minor modification in varieties with outcomes of specific merit or utility, detecting distinctness between varieties may become increasingly challenging. This, together with the ever-increasing number of varieties with which to compare new candidate varieties, supports the potential utility of using DNA-based approaches in variety description.

Molecular Characterization of 87 Functional Genes in Wheat Diversity Panel and Their Association With Phenotypes Under Well-Watered and Water-Limited Conditions

Modern breeding imposed selection for improved productivity that largely influenced the frequency of superior alleles underpinning traits of breeding interest. Therefore, molecular diagnosis for the allelic variations of such genes is important to manipulate beneficial alleles in wheat molecular breeding. We analyzed a diversity panel largely consisted of advanced lines derived from synthetic hexaploid wheats for allelic variation at 87 functional genes or loci of breeding importance using 124 high-throughput KASP markers. We also developed two KASP markers for water-soluble carbohydrate genes (TaSST-D1 and TaSST-A1) associated with plant height and thousand grain weight (TGW) in the diversity panel. KASP genotyping results indicated that beneficial alleles for genes underpinning flowering time (Ppd-D1 and Vrn-D3), thousand grain weight (TaCKX-D1, TaTGW6-A1, TaSus1-7B, and TaCwi-D1), water-soluble carbohydrates (TaSST-A1), yellow-pigment content (Psy-B1 and Zds-D1), and root lesion nematodes (Rlnn1) were fixed in diversity panel with frequency ranged from 96.4 to 100%. The association analysis of functional genes with agronomic and biochemical traits under well-watered (WW) and water-limited (WL) conditions revealed that 21 marker-trait associations (MTAs) were consistently detected in both moisture conditions. The major developmental genes such as Vrn-A1, Rht-D1, and Ppd-B1 had the confounding effect on several agronomic traits including plant height, grain size and weight, and grain yield in both WW and WL conditions. The accumulation of favorable alleles for grain size and weight genes additively enhanced grain weight in the diversity panel. Graphical genotyping approach was used to identify accessions with maximum number of favorable alleles, thus likely to have high breeding value. These results improved our knowledge on the selection of favorable and unfavorable alleles through unconscious selection breeding and identified the opportunities to deploy alleles with effects in wheat breeding.

Genetic architecture of grain yield in bread wheat based on genome-wide association studies

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.

TaBT1, affecting starch synthesis and thousand kernel weight, underwent strong selection during wheat improvement

BRITTLE1 (BT1), responsible for unidirectional transmembrane transport of ADP-glucose, plays a pivotal role in starch synthesis of cereal grain. In this study, we isolated three TaBT1 homoeologous genes located on chromosomes 6A, 6B, and 6D in common wheat. TaBT1 was mainly expressed in developing grains, and knockdown of TaBT1 in common wheat produced a decrease in grain size, thousand kernel weight (TKW), and grain total starch content. High diversity was detected at the TaBT1-6B locus, with 24 polymorphic sites forming three haplotypes (Hap1, Hap2, and Hap3). Association analysis revealed that Hap1 and Hap2 were preferred haplotypes in modern breeding, for their significant correlations with higher TKW. Furthermore, β-glucuronidase (GUS) staining and enzyme activity assays in developing grains of transgenic rice with exogenous promoters indicated that the promoters of Hap1 and Hap2 showed stronger driving activity than that of Hap3. Evolutionary analysis revealed that BT1 underwent strong selection during wheat polyploidization. In addition, the frequency distribution of TaBT1-6B haplotypes revealed that Hap1 and Hap2 were preferred in global modern wheat cultivars. Our findings suggest that TaBT1 has an important effect on starch synthesis and TKW, and provide two valuable molecular markers for marker assisted selection (MAS) in wheat high-yield breeding.

From markers to genome-based breeding in wheat

Recent technological advances in wheat genomics provide new opportunities to uncover genetic variation in traits of breeding interest and enable genome-based breeding to deliver wheat cultivars for the projected food requirements for 2050. There has been tremendous progress in development of whole-genome sequencing resources in wheat and its progenitor species during the last 5 years. High-throughput genotyping is now possible in wheat not only for routine gene introgression but also for high-density genome-wide genotyping. This is a major transition phase to enable genome-based breeding to achieve progressive genetic gains to parallel to projected wheat production demands. These advances have intrigued wheat researchers to practice less pursued analytical approaches which were not practiced due to the short history of genome sequence availability. Such approaches have been successful in gene discovery and breeding applications in other crops and animals for which genome sequences have been available for much longer. These strategies include, (i) environmental genome-wide association studies in wheat genetic resources stored in genbanks to identify genes for local adaptation by using agroclimatic traits as phenotypes, (ii) haplotype-based analyses to improve the statistical power and resolution of genomic selection and gene mapping experiments, (iii) new breeding strategies for genome-based prediction of heterosis patterns in wheat, and (iv) ultimate use of genomics information to develop more efficient and robust genome-wide genotyping platforms to precisely predict higher yield potential and stability with greater precision. Genome-based breeding has potential to achieve the ultimate objective of ensuring sustainable wheat production through developing high yielding, climate-resilient wheat cultivars with high nutritional quality.

Global status of 47 major wheat loci controlling yield, quality, adaptation and stress resistance selected over the last century

BACKGROUND

Wheat breeding over the last 100 years has increased productivity by adapting genotypes to local conditions, but the genomic changes and selection signals that caused phenotypic change during breeding are essentially unknown. Studying and understanding human selection of multiple important genes controlling key phenotypic traits will promote wheat molecular breeding.

RESULTS

A total of 1152 diverse global wheat materials were genotyped based on KASP markers from 47 genes controlling grain yield, grain quality, adaptation, and stress resistance. Significant phenotypic variations between landraces and modern cultivars were found in 11 adaptive and yield-related traits. Thirty-six improvement-selective favorable alleles, including 22 positive prolonged and 14 negative selection alleles, were identified through comparing frequency spectra. Sus1-7A-Hap-H, Sus1-7B-Hap-T, Sus2-2A-Hap-A, TGW6-A1a, Cwi-4A-Hap-C, vrn-A1, PHS1-PHS+ and Lr34+ were subjected to strong selection, and overwhelmingly strong selection had occurred before improvement selection at Psy-A1b, Psy-B1a or b, Psy-D1a and Cwi-5D-Hap-C. However, Rht-B1b, Rht-D1b and 1BL.1RS were rare or absent in Chinese landraces but present in modern Chinese cultivars and introduced accessions. Importantly, Lr68+, Fhb1+, Wx-B1b and Yr15+, currently existing at a low frequency, should be regarded as further major improvement targets in global wheat breeding. Gene flow analysis showed that introduced cultivars especially from the former USSR and Italy contributed to enriched genetic variation in modern Chinese cultivars.

CONCLUSIONS

This work objectively reports human selection on favorable alleles of multiple crucial genes in Asia, Europe, North America and CIMMYT, and traces the distribution of important genes in global wheat for molecular breeding.

Detecting Large Chromosomal Modifications Using Short Read Data From Genotyping-by-Sequencing

Markers linked to agronomic traits are of the prerequisite for molecular breeding. Genotyping-by-sequencing (GBS) data enables to detect small polymorphisms including single nucleotide polymorphisms (SNPs) and short insertions or deletions (InDels) that can be used, for instance, for marker-assisted selection, population genetics, and genome-wide association studies (GWAS). Here, we aim at detecting large chromosomal modifications in barley and wheat based on GBS data. These modifications could be duplications, deletions, substitutions including introgressions as well as alterations of DNA methylation. We demonstrate that GBS coverage analysis is capable to detect Hordeum vulgare/Hordeum bulbosum introgression lines. Furthermore, we identify large chromosomal modifications in barley and wheat collections. Hence, large chromosomal modifications, including introgressions and copy number variations (CNV), can be detected easily and can be used as markers in research and breeding without additional wet-lab experiments.

HD-Marker: a highly multiplexed and flexible approach for targeted genotyping of more than 10,000 genes in a single-tube assay

Targeted genotyping of transcriptome-scale genetic markers is highly attractive for genetic, ecological, and evolutionary studies, but achieving this goal in a cost-effective manner remains a major challenge, especially for laboratories working on nonmodel organisms. Here, we develop a high-throughput, sequencing-based GoldenGate approach (called HD-Marker), which addresses the array-related issues of original GoldenGate methodology and allows for highly multiplexed and flexible targeted genotyping of more than 12,000 loci in a single-tube assay (in contrast to fewer than 3100 in the original GoldenGate assay). We perform extensive analyses to demonstrate the power and performance of HD-Marker on various multiplex levels (296, 795, 1293, and 12,472 genic SNPs) across two sequencing platforms in two nonmodel species (the scallops Chlamys farreri and Patinopecten yessoensis), with extremely high capture rate (98%-99%) and genotyping accuracy (97%-99%). We also demonstrate the potential of HD-Marker for high-throughput targeted genotyping of alternative marker types (e.g., microsatellites and indels). With its remarkable cost-effectiveness (as low as $0.002 per genotype) and high flexibility in choice of multiplex levels and marker types, HD-Marker provides a highly attractive tool over array-based platforms for fulfilling genome/transcriptome-wide targeted genotyping applications, especially in nonmodel organisms.