博文
小麦 PAG 2018 摘要 （五）
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118 Genome-Specific Amplicon Sequencing Strategy Provides Robust Markers across D Genome in Allohexaploid Wheat
Institute of Crop Science, National Agriculture and Food Research Organization (NARO)Tohoku Agricultural Research Center, National Agriculture and Food Research Organization (NARO)
In allohexaploid wheat, array-based genotyping platforms have been widely used for genetic analyses. However, when commercially available arrays were applied for Japanese varieties, there was a low rate of polymorphism and biased distribution of markers across the genomes, especially the D genome. These results indicate that our materials are genetically distant from those used to design the arrays. To increase genome-wide mapping markers suitable for our materials, we have established an efficient procedure to detect nucleotide polymorphisms, and a robust method for genotyping by sequencing genome and site-specific amplicons. Here we present the procedure focusing on the D genome. By sequence capture and next-generation sequencing, 12,551 polymorphisms between wheat varieties ‘Hatsumochi’ and ‘Kitahonami’ were detected across the three genomes. The flanking sequences of target polymorphisms were blasted against the International Wheat Genome Sequencing Consortium survey sequences, and three homoeologous sequences were identified. Based on the polymorphisms among the genomes, 396 D genome-specific primer pairs were designed using an in-house Java pipeline. Approximately 80% of the designed primers successfully amplified genome-specific products, indicating that they could be genotyped as easily as a diploid species. Linkage maps of recombinant inbred lines between the two varieties revealed that the newly developed markers were uniformly distributed across the D genome and greatly extended the total coverage. This result proved that the strategy described here can be useful to increase the number of markers at target sites. This work was supported by grants from the Ministry of Agriculture, Forestry and Fisheries of Japan (NGB1002, NGB1007).
119 Breeding Strategies using Genomic Selection Increase Genetic Gain in Wheat Breeding Programs
Molecular Biology and Genetics, Aarhus University
The traditional wheat breeding programs have been running for several years yet the genetic gain has been very limited. However, the use of genomic information for a selection criterion can increase genetic gain. This study was set to see how much genetic gain can be increased by implementing genomic selection on traditional wheat breeding program. In addition, we investigated the effect of genetic correlation between different traits on genetic gain. A series of wheat breeding programs that run simultaneously for 30 years was simulated using stochastic simulation, meaning each year a new breeding program starts with a cross of 60 parental lines followed by six generations of selfing. Selection was performed on three different generations. At F2, phenotypic selection was performed on breeder’s visual preference. At F5 and F6, either phenotype or Genomic Estimated Breeding Value (GEBV) was used to select on yield. Yield at F5 and F6 was considered as different traits because they differ in plot size, population density, and number of plot replications. Plot heritability of these traits were 0.1, 0.2, and 0.3 while the economic values were 0, 0, and 1. In addition, we simulated different levels (0.3, 0.5, 0.7, 0.9) of genetic correlation between F2 and F5 as well as between F5 and F6. The varied selection criterion and varied genetic correlations make a total of 16 scenarios. GEBV as a selection criterion significantly increased genetic gain by 10% compared to phenotype. Besides, the genetic gain was higher with the higher genetic correlation between traits.
120 Genomic Selection for End-Use Quality Traits in Soft White Wheat (Triticum aestivum L.)
Washington State University
End-use quality traits in soft white wheat are complex traits that are controlled by multiple genetic factors with minor effects. A previous genome-wide association study (GWAS) identified 105 SNP markers for end-use quality traits but these markers only explained 5 – 30% of the phenotypic variation leaving a larger portion of unaccounted heritability. Genomic selection (GS) is a breeding method to predict breeding values using genome-wide markers. GS can simultaneously model all additive genetic variance that is unaccounted for in GWAS. We assessed the application of GS for 21 end-use quality traits using a panel of 469 elite soft white winter wheat from Pacific Northwest breeding programs that were genotyped with 15,229 SNP markers. Genomic prediction using single and multi-trait models were evaluated using the R packages rrBLUP and PHENIX, respectively. Single trait prediction estimates were calculated using the gBLUP model. The multi-trait model used genetic information from the kinship matrix and trait correlation to estimate genomic estimated breeding values (GEBVs). Prediction accuracies following a 10-fold cross validation were 30 – 87% for the single trait model and 69 – 99% for the multi-trait model. Prediction accuracies were significantly higher (up to a 100% increase) in the multi-trait model especially for low heritability traits. Our results suggest that genomic selection can be an efficient tool to develop soft white wheat with superior end-use quality traits. We are currently validating the multi-trait GS model to predict end-use quality performance in different breeding populations (e.g. F5 single plots and double haploids) using genotype-by-sequencing data.
121 Fine Mapping a Major QTL Controlled Tiller Number and Plant Height Using a Wheat660K SNP Array
Nanjing Agricultural University
Tiller number and plant height are two major agronomic traits in cereal crops affecting plant architecture and grain yield. NAUH167, a mutant of common wheat landrace Wangshuibai induced by ethylmethyl sulfide (EMS) treatment, exhibits higher tiller number and reduced plant height. A stable major QTL designated QHt.nau-2D controlling plant height and tiller number, was mapped to the short arm of chromosome 2D flanked by markers QHT239 and QHT187 covering a predicted physical distance of 6.77 Mb. To further map the QHt.nau-2D loci, a population consisted of 6009 F2 progeny from a cross 2011I-78 /NAUH167 was constructed. At the same time, additional molecular markers were developed to saturate the QHt.nau-2D region based on the Wheat660K SNP array. On the basis of Chinese Spring sequences, 53 ARMS-PCR and 18 CAPS/dCAPS markers were designed to detect the polymorphism between 2011I-78 and NAUH167. Finally, QHt.nau-2D was located within a genetic region of 0.5 cM between markers QHT239 and SNP17 spanning a 1.22 Mb physical genomic region of Ae. tauschiichromosome 2DS. The genetic and physical maps of *QHt.nau-2D *provide a framework for map-based cloning and this research would facilitate the characterization of plant height and tiller number in wheat.
122 Survey Sequencing of Flow-Sorted H**aynaldia villosa Chromosome 6VS
Nanjing Agricultural University
Haynaldia villosa has been recognized as a useful germplasm for wheat breeding and improvement and the availability of genomic sequence would accelerate its research and application. In the present work, the short arm of H.** **villosa chromosome 6V in which powdery mildew resistant gene Pm21 have been mapped was flow-sorted by flow cytometry from a telocentric chromosome addition line of 6VS and sequenced using Illumina platform. We obtained a total of 47.7Gb raw sequencing reads and by de novo assembly 230.39Mb assembled sequence. Repetitive elements account for about 74.91% of the genome. 3,276 genes were annotated in the coding fraction of the genome which account for about 2.1%. The syntenic regions of 6VS genes were searched and identified on wheat group 6 chromosomes 6AS, 6BS, 6DS, rice chromosome 2, Brachypodium chromosome 3, and sorghum chromosome 4. Based on the size difference of intron for the synteny genes among 6VS genome and wheat group 6 chromosomes, we designed 222 IT markers, in which 120 markers had specific amplification on 6VS genome.The preliminary genomic sequence of 6VS provides genetic information for cloning genes on this chromosome and developing IT markers for molecular marker assisted breeding and physical map construction.
123 Speed Breeding with Genomic Selection to Accelerate Wheat Variety Development
The University of Queensland
Genomic selection (GS) in wheat could accelerate yield gain principally through a reduction in breeding cycle duration. A method for rapid generation advance called ‘speed breeding’ (SB) enables up to six generations of spring wheat per year, and could be used to accelerate breeding population development and be combined with GS in various breeding schemes to enable even further gains. To improve the accuracy of selection for improved yields, many heritable traits that are genetically correlated with yield could be measured in the field and used in multi-trait models to improve genetic gain (over that of traditional single-trait models only containing yield data of the training population). To test these hypotheses, a 260 multi-parent spring wheat population, genotyped with 8,000 DArT polymorphic markers, underwent yield trials over three years. Trial plots were also phenotyped for height and normalized difference vegetation index (NDVI) using a hand-held GreenSeeker sensor. Yield prediction accuracy was accessed using five-fold cross validation and predicting into different years. Results indicate multi-trait GS prediction including field proxy traits improved selection for field-based yield over that of single-trait models. These traits could be phenotyped in the field following rapid line development under SB and used with training population yield data to advance genetic gain and wheat variety development.
124 High Level of Structural and Sequence Divergence between Homologous Regions of Bread Wheat and T. militinae within the Powdery Mildew Resistance Locus Qpm.Tut-4A
Institute of Experimental Botany
Introgression of QPm.tut-4A locus from Triticum militinae into the distal end of bread wheat chromosome 4AL confers improved resistance against powdery mildew. The locus was high-density mapped and delimited to 0.024 cM using 8327 individuals and 75 markers. Using additional 2052 ph1 *lines seven new recombinations were identified. After chromosome walking, final flanking markers *owm169 *and *owm228 were mapped and the region was found 640.8 kbp and 480.2 kbp long in cv. Chinese Spring (CS) and *T. militinae *(TM), respectively. The cM/Mb ratio is much smaller compared to these commonly found at the end of wheat chromosomes. The sequenced region was annotated and 16 and 12 protein coding genes were identified in CS and TM, respectively. Out of them, seven CS and six TM genes were not syntenic. Furthermore, intergenic regions do not show a significant similarity between CS and TM. The TM region containing the remaining six genes has a syntenic counterpart in CS, but that region was duplicated and one of the duplications was inverted. The duplication and inversion were accompanied by gene loss and four of the TM genes have their counterparts in both duplicated regions in CS. Finally, three genes from the CS region do not have their homologs in the TM region. These structural and sequence differences are major reasons for the discrepancy between the expected and observed cM/Mb ratio. This work was supported by award LO1204 from the National Program of Sustainability I and by the Estonian Ministry of Agriculture.
125 Technologies to Increase Genetic Potential Productivity Under Abiotic Stress for Winter Wheat and Barley Crops, in Climatic Condition from Braila Plain, Romania
BRAICOOP Agricultural Cooperative - Research DepartmentAgricultural Research and Development Station
Each agricultural crop has a theoretical genetic potential, which is represented by the production quantity and quality obtained by the variety of culture, in perfect condition. But perfect conditions for culture there are in few places, especially lately, when seen increasingly accelerated phenomenon of climate change. Increasing theoretical genetic potential for productivity was achieved for each species grown in many years of genetic research, both in the laboratory and in the field experiences. Every year is putting out more and more performing varieties with increased resistance to drought, heat, pests and diseases etc. But genetic potential to the maximum occurs when growing conditions are as close genetically programmed requirements. The abiotic stress can significantly reduces the genetic productivity potential from the very early stages of germination and the vegetation, if the conditions are not fulfilled optimum microclimate (humidity, temperature, nutrients, absence of pests and diseases, etc.). On the other hand, even if the plant grew and developed normally, but is attacked by diseases or pests in a phase of vegetation close to reproduction, this can significantly reduce production unless corrective measures and effective protection of agricultural crops. This paper presents the results about monitoring of genetic potential at some winter wheat and barley varieties, and the results of agrophytotechnical methods to increase genetic potential on production and product quality. The experiments during in the period 2012 - 2017, at Agricultural Research and Development Station of Braila, Romania, by comparing the genetic production potential of some varieties of wheat and barley under different densities and dates of sowing, different fertilization (chemical and biological), and the application of plant biostimulators, also.
126 Structural Organization and Gene Duplication in the Chromosomal Region Harboring the Alpha-Gliadin Gene Family in Aegilops tauschii
USDA ARS, Western Regional Research Center
Among the wheat prolamins important for its end-use traits, α-gliadins are the most abundant and also a major cause of food-related allergies and intolerances. Previous studies of various wheat species estimated between 25 to 150 α-gliadin genes reside in the Gli-2 locus regions. To better understand the evolution of this complex gene family, the DNA sequence of a 1.75-Mb genomic region spanning the Gli-2locus was analyzed in the diploid grass, Aegilops tauschii, the ancestral source of D genome in hexaploid bread wheat. Comparison with orthologous regions from rice, sorghum, and Brachypodium revealed rapid and dynamic changes only occurring to the Ae. tauschii Gli-2region, including insertions of high numbers of non-syntenic genes and a high rate of tandem gene duplications, the latter of which have given rise to 12 copies of α-gliadin genes clustered within a 550-kb region. Among them, five copies have undergone pseudogenization by various mutation events. Insights into the evolutionary relationship of the duplicated α-gliadin genes were obtained from their genomic organization, transcription patterns, transposable element insertions, and phylogenetic analyses. An ancestral GLR gene encoding putative amino acid sensor in all four grass species has duplicated only in Ae. tauschii and generated three more copies that are interspersed with the α-gliadin genes. Phylogenetic inference and different gene expression patterns support functional divergence of the Ae. tauschiiGLRcopies after duplication. Our results suggest that the duplicates of α-gliadin and GLR genes have likely taken different evolutionary paths; conservation for the former and neofunctionalization for the latter.
127 Comparison of Durum Landraces with Northern Great Plains Adapted Cultivars and Identification of Selection Sweeps
North Dakota State University
Durum wheat (T. turgidum ssp. Durum, AABB) is a key crop for high-value food production. Modern breeding programs over the last century have developed a number of elite cultivars that are adapted for growth in the Northern Great Plains. To investigate the genomics underlying this adaptation, we compare 449 global durum lines from the Wheat Coordinated Agricultural Project with 34 advanced lines from the North Dakota State University (NDSU) Durum Breeding Program. We used genotype-by-sequencing (GBS) to identify 21,030 single nucleotide polymorphisms (SNP)s in the populations and measured genetic diversity on several scales. We find that population sub-structure designations largely agree with regional adaptation, and lines adapted to the Northern Great Plains show relatively low genetic diversity and high allelic fixation. We identified 23 genetic intervals that display differential allelic fixation between un-adapted and improved lines, suggesting that these linkage blocks are important for durum improvement. Screening potential lines for these linkage blocks could accelerate breeding efforts, and understanding the genes in these regions could shed light on the molecular characteristics of "elite" lines.
128 PolySNP: An R Package for Calling Polyploid SNP Array Data using Gaussian Mixture Models
Washington State University
The genomic complexity in polyploid plant species makes genotype calling difficult when processing data generated from a high-density SNP array. We present a novel computational method and a software package for calling genotypes from raw hexaploid wheat data generated using the 9k iSelect® assay previously developed for wheat. This method involves fitting an indeterminatenumber of Gaussian mixture components and identifying the optimal number of clusters using an EM-like algorithm implemented in the 'Rmixmod' package. Then markers with bi-allelic patterns are further analyzed by merging outlier clusters and identifying heterozygous clusters. Genotypes are then called based on cluster assignment. Furthermore, models generated with a diverse population can be later used to call genotypes for smaller populations, drastically reducing computational complexity for subsequent calls. This method was tested using a diverse wheat population (n = 1654) and resulting genotypes were compared to previously called genotypes using the current standard method of manual curation. Genomic predictions were generated for both genotype sets using the gBLUP method implemented in the 'rrBLUP' package in R for five different phenotypes. Regression coefficients for predicted vs observed values were improved by 1.38% when using genotypes generated with this new method. Despite an increased computational cost of using Gaussian mixture models, a reduced supervision requirement and increased ability to resolve complex signal patterns allow it to generate more predictive genotypes with less manual manipulation.
129 Genotypic and Phenotypic Evaluation of Preharvest Sprouting in Two and Six Row Barley
USDA, ARS, MWA, Cereal Crops Research Unit, Madison, WI
Preharvest Sprouting (PHS) is a problem negatively affecting both yields and quality of cereal crops grown world-wide. Preharvest Sprouting can be generalized as the propensity of a seed to begin germination while still on the parent plant and is most widely observed in regions with high humidity and/or excessive periods of rain. Barley with signs of PHS is rejected for malt and can only be sold as feed, results in a loss to the grower of about half the value. Preharvest sprouting is a complex trait involving contributions from both multi-genic and environmental factors. Recently, a gene (TaPHS1), was described in Triticum aestivum *(wheat) whose variable genotype and specific gene expression were associated with wheat lines that show either resistance or susceptibility to PHS. Here we present the exonic sequencing and genotypic characterization of the barley (Hordeum vulgare) homolog *HvPHS1 in over 120 barley lines. Additionally, we evaluated each of these lines for dormancy using standard germination tests and also for PHS by challenging intact heads to sprout in an artificial rain chamber.
130 Mining Natural Variation in Triticeae to Improve Plant Immunity
John Innes Centre
It is widely acknowledged that during domestication many crops went through a genetic bottleneck leading to loss of large parts of intraspecific diversity. Modern agriculture therefore seeks to recruit genetic diversity from wild relatives to improve crops. One important area of crop improvement is breeding for resilience to biotic stress. Mining resistance genes from crop wild relatives, however, is a laborious endeavour due to their poor agronomy, ploidy differences, and limited genomic resources. Gene cloning projects are usually long procedures involving the creation of populations dedicated to only a single gene. Here we report Association Genetics using Resistance gene ENrichment SEQuencing (AgRenSeq) to rapidly clone resistance genes from a wild diversity panel through association genomics of selectively captured and sequenced resistance gene analogues. We demonstrate our concept by mining a panel of 151 accessions of Aegilops tauschii, a wild relative of wheat, for resistance genes against the wheat stem rust causing fungus Puccinia graminis f. sp. tritici.
https://blog.sciencenet.cn/blog-1094241-1094519.html
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