Participación de la familia génica GPC sobre la concentración de proteínas y nutrientes en el grano y su relación con la senescencia foliar en plantas de trigo

La removilización de nutrientes al grano y la senescencia son procesos extremadamente interconectados en trigo que determinan la calidad nutricional y panadera. Mientras que el nitrógeno (N) afecta la concentración de proteínas en grano (CPG), en donde alta CPG generan productos panificables con una calidad superior, los micronutrientes como el hierro (Fe) y el Zinc (Zn) afectan la calidad nutricional. Por lo tanto, el mejoramiento de la calidad en trigo requiere un profundo entendimiento de las redes génicas que regulan y controlan la senescencia y la removilización de nutrientes al grano. El gen GPC-B1, proveniente del trigo silvestre Triticum turgidum var. diccocoides, pertenece a la familia de factores de transcripción NAC y es la primer fuente de variación para CPG y micronutrientes identificada en trigo. Los objetivos de esta tesis fueron: estudiar el efecto de la introgresión de GPC-B1 sobre la CPG, concentración de micro y macronutrientes y diferentes parámetros agronómicos en germoplasma argentino; profundizar, mediante análisis transcriptómicos y el uso de plantas mutantes para los genes GPC el entendimiento de la regulación génica que ocurre durante la senescencia y finalmente identificar nuevos genes de transporte de N, Fe y Zn al grano mediante genómica comparativa con arroz. Cuando GPC-B1 se introdujo en germoplasma de origen argentino la CPG se incrementó entre 3 a 8,11 g kg-1 a través de diferentes cultivares y ambientes. A pesar del efecto negativo del gen sobre el tamaño de granos y una aceleración en la senescencia, no se observaron diferencias significativas en rendimiento. El incremento en la CPG se explicó por una mayor proteólisis y eficiencia en el transporte de aminoácidos al grano. Cuando se analizó la concentración de nutrientes, se observaron incrementos consistentes en Fe. La combinación de análisis transcriptómicos y plantas mutantes permitió identificar 3888 genes diferencialmente expresados durante la senescencia y 340 genes modulados por la familia GPC. A su vez, se han identificado 21 genes relacionados con el transporte de N al grano y se han caracterizado nueve familias génicas relacionadas con el transporte de Fe y Zn al grano que pueden utilizarse en programas de mejoramiento para incrementar la calidad nutricional en trigo

Transcriptional signatures of wheat inforescence development

In order to maintain global food security, it will be necessary to increase yields of the cereal crops that provide most of the calories and protein for the world’s population, which includes common wheat (Triticum aestivum L.). An important wheat yield component is the number of grain-holding spikelets which form on the spike during inflorescence development. Characterizing the gene regulatory networks controlling the timing and rate of inflorescence development will facilitate the selection of natural and induced gene variants that contribute to increased spikelet number and yield. In the current study, co-expression and gene regulatory networks were assembled from a temporal wheat spike transcriptome dataset, revealing the dynamic expression profiles associated with the progression from vegetative meristem to terminal spikelet formation. Consensus co-expression networks revealed enrichment of several transcription factor families at specific developmental stages including the sequential activation of different classes of MIKC-MADS box genes. This gene regulatory network highlighted interactions among a small number of regulatory hub genes active during terminal spikelet formation. Finally, the CLAVATA and WUSCHEL gene families were investigated, revealing potential roles for TtCLE13, TtWOX2, and TtWOX7 in wheat meristem development. The hypotheses generated from these datasets and networks further our understanding of wheat inflorescence development. IntroductionFil: VanGessel, Carl. Colorado State University; Department of Soil and Crop Sciences; Estados UnidosFil: Hamilton, James. Colorado State University; Department of Soil and Crop Sciences; Estados UnidosFil: Tabbita, Facundo. Universidad de Córdoba. Escuela Técnica Superior de Ingeniería Agronómica y de Montes. Departamento de Genética; España. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; ArgentinaFil: Dubcovsky, Jorge. University of California, Department of Plant Sciences; Estados Unidos. Howard Hughes Medical Institute; Estados UnidosFil: Pearce, Stephen. Rothamsted Research. Sustainable Soils and Crops; Reino Unido. Colorado State University; Department of Soil and Crop Sciences; Estados Unido

Allelic Variation of Puroindolines Genes in Iranian Common Wheat Landraces

Wheat is one of the most widely grown crops in the world. One of the traits that defines wheat quality is grain hardness, which is determined by puroindolines (PINA and PINB) proteins encoded with Pina-D1 and Pinb-D1 genes. In this study, the diversity of Pina-D1 and Pinb-D1 was evaluated in a collection of 271 Iranian common wheat (Triticum aestivum L. ssp. aestivum) landraces, whose kernels had previously been classified as hard or semi-hard based on PSI analysis. Three alleles previously described as associated with hard grain were detected in the collection: Pinb-D1b in 11 accessions, Pinb-d1ab in 175 accessions, and Pinb-d1p in 80 accessions. In addition, a novel allele tentatively named Pinb-d1ak was detected in Pinb-D1 and was characterized by a change at position 140 of the deduced protein (cysteine/tyrosine). On average, the accessions with this allele showed a lower PSI value than the accessions with other Pin allele. This means that this novel allele may be associated with harder grains than other Pin alleles and could be used by breeding programs targeting different grain hardness levels. This study highlights the importance of conserving and characterizing wheat genetic resources that could be used as sources of genetic variability in breeding programs

Regulation of Zn and Fe transporters by the GPC1 gene during early wheat monocarpic senescence

BACKGROUND: During wheat senescence, leaf components are degraded in a coordinated manner, releasing amino acids and micronutrients which are subsequently transported to the developing grain. We have previously shown that the simultaneous downregulation of Grain Protein Content (GPC) transcription factors, GPC1 and GPC2, greatly delays senescence and disrupts nutrient remobilization, and therefore provide a valuable entry point to identify genes involved in micronutrient transport to the wheat grain. RESULTS: We generated loss-of-function mutations for GPC1 and GPC2 in tetraploid wheat and showed in field trials that gpc1 mutants exhibit significant delays in senescence and reductions in grain Zn and Fe content, but that mutations in GPC2 had no significant effect on these traits. An RNA-seq study of these mutants at different time points showed a larger proportion of senescence-regulated genes among the GPC1 (64%) than among the GPC2 (37%) regulated genes. Combined, the two GPC genes regulate a subset (21.2%) of the senescence-regulated genes, 76.1% of which are upregulated at 12 days after anthesis, before the appearance of any visible signs of senescence. Taken together, these results demonstrate that GPC1 is a key regulator of nutrient remobilization which acts predominantly during the early stages of senescence. Genes upregulated at this stage include transporters from the ZIP and YSL gene families, which facilitate Zn and Fe export from the cytoplasm to the phloem, and genes involved in the biosynthesis of chelators that facilitate the phloem-based transport of these nutrients to the grains. CONCLUSIONS: This study provides an overview of the transport mechanisms activated in the wheat flag leaf during monocarpic senescence. It also identifies promising targets to improve nutrient remobilization to the wheat grain, which can help mitigate Zn and Fe deficiencies that afflict many regions of the developing world.Fil: Pearce, Stephen. University of California; Estados UnidosFil: Tabbita, Facundo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación de Recursos Naturales. Instituto de Recursos Biológicos; ArgentinaFil: Cantu, Dario. University of California; Estados UnidosFil: Buffalo, Vince. University of California; Estados UnidosFil: Avni, Raz. Tel Aviv University; IsraelFil: Vazquez Gross, Hans. University of California; Estados UnidosFil: Zhao, Rongrong. China Agricultural University; ChinaFil: Conley, Christopher J.. University of California; Estados UnidosFil: Distelfeld, Assaf. Faculty Of Life Sciences, Department Of Molecular Biolo;Fil: Dubcovsky, Jorge. University of California; Estados Unidos. Howard Hughes Medical Institute ; Estados Unidos. Gordon & Betty Moore Foundation Investigator; Estados Unido

On-farm impact on bread wheat quality under different management practices: a case study in the Yaqui Valley

Continuous development of new wheat varieties is necessary to satisfy the demands of farmers, industry, and consumers. The evaluation of candidate genotypes for commercial release under different on-farm conditions is a highly recommended strategy to assess the performance and stability of new cultivars in heterogeneous environments and different farming systems. The main objectives of this study were to evaluate the grain yield and quality performance of ten different genotypes across six contrasting farmers’ field conditions, determined by different irrigation and nitrogen fertilization levels, and to develop suggestions to aid breeding programs and farmers for a more efficient use of resources. Through Genotype and Genotype by Environment (GGE) interaction biplot analyses we identified the genotypes with the highest performance and stability in the Yaqui Valley.Instituto de Recursos BiológicosFil: Tabbita, Facundo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina. Universidad de Córdoba, Departamento de Genética, Escuela Técnica Superior de Ingeniería Agronómica y de Montes; ArgentinaFil: Ortiz-Monasterio, Iván. International Maize and Wheat Improvement Center (CIMMYT); MéxicoFil: Piñera-Chávez, Francisco J. International Maize and Wheat Improvement Center (CIMMYT); MéxicoFil: Ibba, María Itria. International Maize and Wheat Improvement Center (CIMMYT); MéxicoFil: Guzman, Carlos. Universidad de Córdoba. Escuela Técnica Superior de Ingeniería Agronómica y de Montes. Departamento de Genética; Españ

On-farm assessment of yield and quality traits in durum wheat

Durum wheat is key source of calories and nutrients for many regions of the world. Demand for it is predicted toincrease. Further efforts are therefore needed to develop new cultivars adapted to different future scenarios. Developing anovel cultivar takes, on average, 10 years and advanced lines are tested during the process, in general, under standardized con-ditions. Although evaluating candidate genotypes for commercial release under different on-farm conditions is a strategy thatis strongly recommended, its application for durum wheat and particularly for quality traits has been limited. This study eval-uated the grain yield and quality performance of eight different genotypes acrossfive contrasting farmers’fields over two sea-sons. Combining different analysis strategies, the most outstanding and stable genotypes were identified.RESULTS: The analyses revealed that some traits were mainly explained by the genotype effect (thousand kernel weight,flour sodiumdodecyl sulfate sedimentation volume, andflour yellowness), others by the management practices (yield and grain protein content),and others (test weight) by the year effect. In general, yield showed the highest range of variation across genotypes, managementpractices, and years and test weight the narrowest range. Flour yellowness was the most stable traitacross management conditions,while yield-related traits were the most unstable. We also determined the most representative and discriminativefield conditions,which is a beneficial strategy when breeders are constrained in their ability to develop multi-environment experiments.CONCLUSIONS: We concluded that assessing genotypes in different farming systems is a valid and complementary strategy foron-station trials for determining the performance of future commercial cultivars in heterogeneous environments to improvethe breeding process and resources.Fil: Tabbita, Facundo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina. Universidad de Córdoba, Departamento de Genética. Escuela Técnica Superior de Ingeniería Agronómica y de Montes; EspañaFil: Ortiz-Monasterio, Iván. International Maize and Wheat Improvement Center (CIMMYT); MéxicoFil: Piñera-Chávez, Francisco J. International Maize and Wheat Improvement Center (CIMMYT); MéxicoFil: Ibba, María Itria. International Maize and Wheat Improvement Center (CIMMYT); MéxicoFil: Guzman, Carlos. Universidad de Córdoba. Escuela Técnica Superior de Ingeniería Agronómica y de Montes. Departamento de Genética; Españ

Separating homeologs by phasing in the tetraploid wheat transcriptome

Citation: Krasileva, K., . . . & Dubcovsky, J. (2013). Separating homeologs by phasing in the tetraploid wheat transcriptome. Genome Biology, 14(6), 1-19. https://doi.org/10.1186/gb-2013-14-6-r66Background: The high level of identity among duplicated homoeologous genomes in tetraploid pasta wheat presents substantial challenges for de novo transcriptome assembly. To solve this problem, we develop a specialized bioinformatics workflow that optimizes transcriptome assembly and separation of merged homoeologs. To evaluate our strategy, we sequence and assemble the transcriptome of one of the diploid ancestors of pasta wheat, and compare both assemblies with a benchmark set of 13,472 full-length, non-redundant bread wheat cDNAs. Results: A total of 489 million 100 bp paired-end reads from tetraploid wheat assemble in 140,118 contigs, including 96% of the benchmark cDNAs. We used a comparative genomics approach to annotate 66,633 open reading frames. The multiple k-mer assembly strategy increases the proportion of cDNAs assembled full-length in a single contig by 22% relative to the best single k-mer size. Homoeologs are separated using a post-assembly pipeline that includes polymorphism identification, phasing of SNPs, read sorting, and re-assembly of phased reads. Using a reference set of genes, we determine that 98.7% of SNPs analyzed are correctly separated by phasing. Conclusions: Our study shows that de novo transcriptome assembly of tetraploid wheat benefit from multiple k-mer assembly strategies more than diploid wheat. Our results also demonstrate that phasing approaches originally designed for heterozygous diploid organisms can be used to separate the close homoeologous genomes of tetraploid wheat. The predicted tetraploid wheat proteome and gene models provide a valuable tool for the wheat research community and for those interested in comparative genomic studies

Functional characterization of GPC-1 genes in hexaploid wheat

In wheat, monocarpic senescence is a tightly regulated process during which nitrogen (N) and micronutrients stored pre-anthesis are remobilized from vegetative tissues to the developing grains. Recently, a close connection between senescence and remobilization was shown through the map-based cloning of the GPC (grain protein content) gene in wheat. GPC-B1 encodes a NAC transcription factor associated with earlier senescence and increased grain protein, iron and zinc content, and is deleted or non-functional in most commercial wheat varieties. In the current research, we identified 'loss of function' ethyl methanesulfonate mutants for the two GPC-B1 homoeologous genes; GPC-A1 and GPC-D1, in a hexaploid wheat mutant population. The single gpc-a1 and gpc-d1 mutants, the double gpc-1 mutant and control lines were grown under field conditions at four locations and were characterized for senescence, GPC, micronutrients and yield parameters. Our results show a significant delay in senescence in both the gpc-a1 and gpc-d1 single mutants and an even stronger effect in the gpc-1 double mutant in all the environments tested in this study. The accumulation of total N in the developing grains showed a similar increase in the control and gpc-1 plants until 25 days after anthesis (DAA) but at 41 and 60 DAA the control plants had higher grain N content than the gpc-1 mutants. At maturity, GPC in all mutants was significantly lower than in control plants while grain weight was unaffected. These results demonstrate that the GPC-A1 and GPC-D1 genes have a redundant function and play a major role in the regulation of monocarpic senescence and nutrient remobilization in wheat.Fil: Avni, Raz. Tel Aviv University; IsraelFil: Zhao, Rongrong. China Agricultural University; República de China. University of California at Davis; Estados UnidosFil: Pearce, Stephen. University of California at Davis; Estados UnidosFil: Jun, Yan. University of Haifa; IsraelFil: Uauy, Cristobal. University of California at Davis; Estados UnidosFil: Tabbita, Facundo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. University of California at Davis; Estados UnidosFil: Fahima, Tzion. University of Haifa; IsraelFil: Slade, Ann. Arcadia Biosciences Inc.; Estados UnidosFil: Dubcovsky, Jorge. University of California at Davis; Estados UnidosFil: Distelfeld, Assaf. Tel Aviv University; Israe