Genome-Wide Association Study Reveals Novel Genomic Regions Associated With High Grain Protein Content in Wheat Lines Derived From Wild Emmer Wheat.
ABSTRACT: Grain protein content (GPC) and yield are of two important traits in wheat, but their negative correlation has hampered their simultaneous improvement in conventional breeding. Wild emmer wheat (Triticum turgidum ssp. dicoccoides) is an important genetic resource for wheat quality improvement. In this study, we report a genome-wide association study (GWAS) using 13116 DArT-seq markers to characterize GPC in 161 wheat lines derived from wild emmer. Using a general linear model, we identified 141 markers that were significantly associated with GPC, and grouped into 48 QTL regions. Using both general linear model and mixed linear model, we identified four significant markers that were grouped into two novel QTL regions on chromosomes 2BS (QGpc.cd1-2B.1) and 7BL (QGpc.cd1-7B.2). The two QTLs have no negative effects on thousand kernel weight (TKW) and should be useful for simultaneous improvement of GPC and TKW in wheat breeding. Searches of public databases revealed 61 putative candidate/flanking genes related to GPC. The putative proteins of interest were grouped in four main categories: enzymes, kinase proteins, metal transport-related proteins, and disease resistance proteins. The linked markers and associated candidate genes provide essential information for cloning genes related to high GPC and performing marker-assisted breeding in wheat.
Project description:<h4>Background</h4>Improvement of wheat gercTriticum aestivum L.) yield could relieve global food shortages. Kernel size, as an important component of 1000-kernel weight (TKW), is always a significant consideration to improve yield for wheat breeders. Wheat related species possesses numerous elite genes that can be introduced into wheat breeding. It is thus vital to explore, identify, and introduce new genetic resources for kernel size from wheat wild relatives to increase wheat yield.<h4>Results</h4>In the present study, quantitative trait loci (QTL) for kernel length (KL) and width (KW) were detected in a recombinant inbred line (RIL) population derived from a cross between a wild emmer accession 'LM001' and a Sichuan endemic tetraploid wheat 'Ailanmai' using the Wheat 55 K single nucleotide polymorphism (SNP) array-based constructed linkage map and phenotype from six different environments. We identified eleven QTL for KL and KW including two major ones QKL.sicau-AM-3B and QKW.sicau-AM-4B, the positive alleles of which were from LM001 and Ailanmai, respectively. They explained 17.57 to 44.28% and 13.91 to 39.01% of the phenotypic variance, respectively. For these two major QTL, Kompetitive allele-specific PCR (KASP) markers were developed and used to successfully validate their effects in three F<sub>3</sub> populations and two natural populations containing a panel of 272 Chinese wheat landraces and that of 300 Chinese wheat cultivars, respectively. QKL.sicau-AM-3B was located at 675.6-695.4 Mb on chromosome arm 3BL. QKW.sicau-AM-4B was located at 444.2-474.0 Mb on chromosome arm 4BL. Comparison with previous studies suggested that these two major QTL were likely new loci. Further analysis indicated that the positive alleles of QKL.sicau-AM-3B and QKW.sicau-AM-4B had a great additive effect increasing TKW by 6.01%. Correlation analysis between KL and other agronomic traits showed that KL was significantly correlated to spike length, length of uppermost internode, TKW, and flag leaf length. KW was also significantly correlated with TKW. Four genes, TRIDC3BG062390, TRIDC3BG062400, TRIDC4BG037810, and TRIDC4BG037830, associated with kernel development were predicted in physical intervals harboring these two major QTL on wild emmer and Chinese Spring reference genomes.<h4>Conclusions</h4>Two stable and major QTL for KL and KW across six environments were detected and verified in three biparental populations and two natural populations. Significant relationships between kernel size and yield-related traits were identified. KASP markers tightly linked the two major QTL could contribute greatly to subsequent fine mapping. These results suggested the application potential of wheat related species in wheat genetic improvement.
Project description:Wheat grain protein content (GPC) and yield components are complex quantitative traits influenced by a multi-factorial system consisting of both genetic and environmental factors. Although seed storage proteins represent less than 15% of mature kernels, they are crucial in determining end-use properties of wheat, as well as the nutritional value of derived products. Yield and GPC are negatively correlated, and this hampers breeding programs of commercially valuable wheat varieties. The goal of this work was the evaluation of genetic variability for quantity and composition of seed storage proteins, together with yield components [grain yield per spike (GYS) and thousand-kernel weight (TKW)] in a durum wheat population obtained by an inter-specific cross between a common wheat accession and the durum cv. Saragolla. Quantitative trait loci (QTL) analysis was conducted and closely associated markers identified on a genetic map composed of 4,366 SNP markers previously obtained in the same durum population genotyped with the 90K iSelect SNP assay. A total of 22 QTL were detected for traits related to durum wheat quality. Six genomic regions responsible for GPC control were mapped on chromosomes 2B, 3A, 4A, 4B, 5B, and 7B, with major QTL on chromosomes 2B, 4A, and 5B. Nine loci were detected for GYS: two on chromosome 5B and 7A and one on chromosomes 2A, 2B, 4A, 4B, 7B, with the strongest QTL on 2B. Eight QTL were identified for TKW, three of which located on chromosome 3A, two on 1B and one on 4B, 5A, and 5B. Only small overlapping was found among QTL for GYS, TKW, and GPC, and increasing alleles coming from both parents on different chromosomes. Good candidate genes were identified in the QTL confidence intervals for GYS and TKW.
Project description:Micronutrient and protein malnutrition is recognized among the major global health issues. Genetic biofortification is a cost-effective and sustainable strategy to tackle malnutrition. Genomic regions governing grain iron concentration (GFeC), grain zinc concentration (GZnC), grain protein content (GPC), and thousand kernel weight (TKW) were investigated in a set of 163 recombinant inbred lines (RILs) derived from a cross between cultivated wheat variety WH542 and a synthetic derivative (<i>Triticum dicoccon</i> PI94624/<i>Aegilops tauschii</i> //BCN). The RIL population was genotyped using 100 simple-sequence repeat (SSR) and 736 single nucleotide polymorphism (SNP) markers and phenotyped in six environments. The constructed genetic map had a total genetic length of 7,057 cM. A total of 21 novel quantitative trait loci (QTL) were identified in 13 chromosomes representing all three genomes of wheat. The trait-wise highest number of QTL was identified for GPC (10 QTL), followed by GZnC (six QTL), GFeC (three QTL), and TKW (two QTL). Four novel stable QTL (<i>QGFe.iari-7D.1, QGFe.iari-7D.2, QGPC.iari-7D.2</i>, and <i>QTkw.iari-7D</i>) were identified in two or more environments. Two novel pleiotropic genomic regions falling between <i>Xgwm350-AX-94958668</i> and <i>Xwmc550-Xgwm350</i> in chromosome 7D harboring co-localized QTL governing two or more traits were also identified. The identified novel QTL, particularly stable and co-localized QTL, will be validated to estimate their effects on different genetic backgrounds for subsequent use in marker-assisted selection (MAS). Best QTL combinations were identified by the estimation of additive effects of the stable QTL for GFeC, GZnC, and GPC. A total of 11 RILs (eight for GZnC and three for GPC) having favorable QTL combinations identified in this study can be used as potential donors to develop bread wheat varieties with enhanced micronutrients and protein.
Project description:Wheat is one of the important staple crops as the resources of both food and micronutrient for most people of the world. However, the levels of micronutrients (especially Fe and Zn) in common wheat are inherently low. Biofortification is an effective way to increase the micronutrient concentration of wheat. Wild emmer wheat (<i>Triticum turgidum</i> ssp. <i>dicoccoides</i>, AABB, 2n = 4x = 28) is an important germplasm resource for wheat micronutrients improvement. In the present study, a genome-wide association study (GWAS) was performed to characterize grain iron, zinc, and manganese concentration (GFeC, GZnC, and GMnC) in 161 advanced lines derived from wild emmer. Using both the general linear model and mixed linear model, we identified 14 high-confidence significant marker-trait associations (MTAs) that were associated with GFeC, GZnC, and GMnC of which nine MTAs were novel. Six MTAs distributed on chromosomes 3B, 4A, 4B, 5A, and 7B were significantly associated with GFeC. Three MTAs on 1A and 2A were significantly associated with GZnC and five MTAs on 1B were significantly associated with GMnC. These MTAs show no negative effects on thousand kernel weight (TKW), implying the potential value for simultaneous improvement of micronutrient concentrations and TKW in breeding. Meanwhile, the GFeC, GZnC and GMnC are positively correlated, suggesting that these traits could be simultaneously improved. Genotypes containing high-confidence MTAs and 61 top genotypes with a higher concentration of grain micronutrients were recommended for wheat biofortification breeding. A total of 38 candidate genes related to micronutrient concentrations were identified. These candidates can be classified into four main groups: enzymes, transporter proteins, MYB transcription factor, and plant defense responses proteins. The MTAs and associated candidate genes provide essential information for wheat biofortification breeding through marker-assisted selection (MAS).
Project description:Genetic dissection kernel weight-related traits is of great significance for improving wheat yield potential. As one of the three major yield components of wheat, thousand kernel weight (TKW) was mainly affected by grain length (GL) and grain width (GW). To uncover the key loci for these traits, we carried out a quantitative trait loci (QTL) analysis of an F<sub>6</sub> recombinant inbred lines (RILs) population derived from a cross of Henong 5290 (small grain) and 06Dn23 (big grain) with a 50 K single nucleotide polymorphism (SNP) array. A total of 17 stable and big effect QTL, including 5 for TKW, 8 for GL and 4 for GW, were detected on the chromosomes 1B, 2A, 2B, 2D, 4B, 5A, 6A and 6D, respectively. Among these, there were two co-located loci for three traits that were mapped on the chromosome 4BS and 6AL. The QTL on 6AL was the most stable locus and explained 15.4-24.8%, 4.1-8.8% and 15.7-24.4% of TKW, GW and GL variance, respectively. In addition, two more major QTL of GL were located on chromosome arm 2BL and 2DL, accounting for 9.7-17.8% and 13.6-19.8% of phenotypic variance, respectively. In this study, we found one novel co-located QTL associated with GL and TKW in 2DL, <i>QGl.haaf-2DL.2</i>/<i>QTkw.haaf-2DL.2</i>, which could explain 13.6-19.8% and 9.8-10.7% phenotypic variance, respectively. Genetic regions and linked markers of these stable QTL will help to further refine mapping of the corresponding loci and marker-assisted selection (MAS) breeding for wheat grain yield potential improvement.
Project description:In the present study, four large-scale field trials using two doubled haploid wheat populations were conducted in different environments for two years. Grain protein content (GPC) and 21 other yield-related traits were investigated. A total of 227 QTL were mapped on 18 chromosomes, which formed 35 QTL clusters. The potential candidate genes underlying the QTL clusters were suggested. Furthermore, adding to the significant correlations between yield and its related traits, correlation variations were clearly shown within the QTL clusters. The QTL clusters with consistently positive correlations were suggested to be directly utilized in wheat breeding, including 1B.2, 2A.2, 2B (4.9-16.5 Mb), 2B.3, 3B (68.9-214.5 Mb), 4A.2, 4B.2, 4D, 5A.1, 5A.2, 5B.1, and 5D. The QTL clusters with negative alignments between traits may also have potential value for yield or GPC improvement in specific environments, including 1A.1, 2B.1, 1B.3, 5A.3, 5B.2 (612.1-613.6 Mb), 7A.1, 7A.2, 7B.1, and 7B.2. One GPC QTL (5B.2: 671.3-672.9 Mb) contributed by cultivar Spitfire was positively associated with nitrogen use efficiency or grain protein yield and is highly recommended for breeding use. Another GPC QTL without negatively pleiotropic effects on 2A (50.0-56.3 Mb), 2D, 4D, and 6B is suggested for quality wheat breeding.
Project description:High-density genetic linkage maps are essential for precise mapping quantitative trait loci (QTL) in wheat (Triticum aestivum L.). In this study, a high-density genetic linkage map consisted of 6312 SNP and SSR markers was developed to identify QTL controlling kernel size and weight, based on a recombinant inbred line (RIL) population derived from the cross of Shixin828 and Kenong2007. Seventy-eight putative QTL for kernel length (KL), kernel width (KW), kernel diameter ratio (KDR), and thousand kernel weight (TKW) were detected over eight environments by inclusive composite interval mapping (ICIM). Of these, six stable QTL were identified in more than four environments, including two for KL (qKL-2D and qKL-6B.2), one for KW (qKW-2D.1), one for KDR (qKDR-2D.1) and two for TKW (qTKW-5A and qTKW-5B.2). Unconditional and multivariable conditional QTL mapping for TKW with respect to TKW component (TKWC) revealed that kernel dimensions played an important role in regulating the kernel weight. Seven QTL-rich genetic regions including seventeen QTL were found on chromosomes 1A (2), 2D, 3A, 4B and 5B (2) exhibiting pleiotropic effects. In particular, clusters on chromosomes 2D and 5B possessing significant QTL for kernel-related traits were highlighted. Markers tightly linked to these QTL or clusters will eventually facilitate further studies for fine mapping, candidate gene discovery and marker-assisted selection (MAS) in wheat breeding.
Project description:The domestication and subsequent genetic improvement of wheat led to the development of large-seeded cultivated wheat species relative to their smaller-seeded wild progenitors. While increased grain weight (GW) continues to be an important goal of many wheat breeding programs, few genes underlying this trait have been identified despite an abundance of studies reporting quantitative trait loci (QTL) for GW. Here we perform a QTL analysis for GW using a population of recombinant inbred lines (RILs) derived from the cross between wild emmer wheat accession 'Zavitan' and durum wheat variety 'Svevo'. Identified QTLs in this population were anchored to the recent Zavitan reference genome, along with previously published QTLs for GW in tetraploid wheat. This genome-based, meta-QTL analysis enabled the identification of a locus on chromosome 6A whose introgression from wild wheat positively affects GW. The locus was validated using an introgression line carrying the 6A GW QTL region from Zavitan in a Svevo background, resulting in >8% increase in GW compared to Svevo. Using the reference sequence for the 6A QTL region, we identified a wheat ortholog to OsGRF4, a rice gene previously associated with GW. The coding sequence of this gene (TtGRF4-A) contains four single nucleotide polymorphisms (SNPs) between Zavitan and Svevo, one of which reveals the Zavitan allele to be rare in a core collection of wild emmer and completely absent from the domesticated emmer genepool. Similarly, another wild emmer accession (G18-16) was found to carry a rare allele of TtGRF4-A that also positively affects GW and is characterized by a unique SNP absent from the entire core collection. These results exemplify the rich genetic diversity of wild wheat, posit TtGRF4-A as a candidate gene underlying the 6A GW QTL, and suggest that the natural Zavitan and G18-16 alleles of TtGRF4-A have potential to increase wheat yields in breeding programs.
Project description:A quantitative trait locus (QTL) controlling wheat grain protein content (GPC) and flour protein content (FPC) was identified using doubled haploid (DH) lines developed from a cross between the hard red winter wheat variety 'Yumechikara' with a high protein content used for bread making, and the soft red winter wheat 'Kitahonami' with a low protein content used for Japanese white salted noodles. A single major QTL, <i>QGpc.2B-yume</i>, was identified on the short arm of wheat chromosome 2<b>B</b> for both the GPC and FPC over 3 years of testing. <i>QGpc.2B-yume</i> was mapped on the flanking region of microsatellite marker <i>Xgpw4382</i>. The DH lines grouped by the haplotype of the closest flanking microsatellite marker <i>Xgpw4382</i> showed differences of 1.0% and 1.1% in mean GPC and FPC, respectively. Yield-component-related traits were not affected by the haplotype of <i>QGpc.2B-yume</i>, and major North American hard red winter wheat varieties showed the high-protein haplotype. Unlike <i>Gpc-B1</i> derived from tetraploid wheat, <i>QGpc.2B-yume</i> has no negative effects on yield-component-related traits and should be useful for wheat breeding to increase GPC and FPC.
Project description:BACKGROUND:Ethylene Responsive Factor (ERF) is involved in various processes of plant development and stress responses. In wheat, several ERFs have been identified and their roles in mediating biotic or abiotic stresses have been elucidated. However, their effects on wheat plant architecture and yield-related traits remain poorly studied. RESULTS:In this study, TaERF8, a new member of the ERF family, was isolated in wheat (Triticum aestivum L.). Three homoeologous TaERF8 genes, TaERF8-2A, TaERF8-2B and TaERF8-2D (named according to sub-genomic origin), were cloned from the common wheat cultivar Chinese Spring. The three homoeologs showed highly similar protein sequences, with identical AP2 domain. Whereas homoeologs sequence polymorphism analysis allowed the establishment of ten, two and three haplotypes, respectively. Expression analysis revealed that TaERF8s were constitutively expressed through entire wheat developmental stages. Analysis of related agronomic traits of TaERF8-2B overexpressing transgenic lines showed that TaERF8-2B plays a role in regulating plant architecture and yield-related traits. Association analysis between TaERF8-2B haplotypes (Hap-2B-1 and Hap-2B-2) and agronomic traits showed that TaERF8-2B was associated with plant height, heading date and 1000 kernel weight (TKW). The TaERF8-2B haplotypes distribution analysis revealed that Hap-2B-2 frequency increased in domesticated emmer wheat and modern varieties, being predominant in five major China wheat producing zones. CONCLUSION:These results indicated that TaERF8s are differentially involved in the regulation of wheat growth and development. Haplotype Hap-2B-2 was favored during domestication and in Chinese wheat breeding. Unveiling that the here described molecular marker TaERF8-2B-InDel could be used for marker-assisted selection, plant architecture and TKW improvement in wheat breeding.