Guihua Bai

Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars

Domesticated crops experience strong human-mediated selection aimed at developing high-yielding varieties adapted to local conditions. To detect regions of the wheat genome subject to selection during improvement, we developed a high-throughput array to interrogate 9,000 gene-associated single-nucleotide polymorphisms (SNP) in a worldwide sample of 2,994 accessions of hexaploid wheat including landraces and modern cultivars. Using a SNP-based diversity map we characterized the impact of crop improvement on genomic and geographic patterns of genetic diversity. We found evidence of a small population bottleneck and extensive use of ancestral variation often traceable to founders of cultivars from diverse geographic regions. Analyzing genetic differentiation among populations and the extent of haplotype sharing, we identified allelic variants subjected to selection during improvement. Selective sweeps were found around genes involved in the regulation of flowering time and phenology. An introgression of a wild relative-derived gene conferring resistance to a fungal pathogen was detected by haplotype-based analysis. Comparing selective sweeps identified in different populations, we show that selection likely acts on distinct targets or multiple functionally equivalent alleles in different portions of the geographic range of wheat. The majority of the selected alleles were present at low frequency in local populations, suggesting either weak selection pressure or temporal variation in the targets of directional selection during breeding probably associated with changing agricultural practices or environmental conditions. The developed SNP chip and map of genetic variation provide a resource for advancing wheat breeding and supporting future population genomic and genome-wide association studies in wheat.

Deoxynivalenol-nonproducing Fusarium graminearum Causes Initial Infection, but does not Cause DiseaseSpread in Wheat Spikes

Fusarium graminearum is a major pathogen that causes fusarium head blight (FHB) in wheat and produces deoxynivalenol (DON) in infected grain. In previous studies, the trichodiene synthase gene (Tri5) in the fungal strain GZ3639 was disrupted to produce the DON-nonproducing strain GZT40.In this report, the virulence of strains GZ3639 and GZT40 was tested on wheat cultivars with various resistance levels by using methods of spray inoculation and injection inoculation with fungal conidia. Under field and greenhouse conditions, strain GZ3639 produced significantly more disease symptoms and reduced more yield than strain GZT40 in all wheat cultivars tested. Conidia of strain GZT40 germinated and infected inoculated spikelets, but disease symptoms were limited to inoculated spikelets without spread to uninoculated spikelets. When strain GZT40 was inoculated using the spray method, multiple initial infection sites in a spike resulted in higher levels of disease symptoms than in spikes inoculated by a single injection. Greenhouse tests confirmed that strain GZT40 did not produce DON in the infected kernels following either inoculation method. The results confirm that DON production plays a significant role in the spread of FHB within a spike, and are the first report that DON production is not necessary for initial infection by the fungus.

Differentially expressed genes between drought-tolerant and drought-sensitive barley genotypes in response to drought stress during the reproductive stage

Drought tolerance is a key trait for increasing and stabilizing barley productivity in dry areas worldwide. Identification of the genes responsible for drought tolerance in barley (Hordeum vulgare L.) will facilitate understanding of the molecular mechanisms of drought tolerance, and also facilitate the genetic improvement of barley through marker-assisted selection or gene transformation. To monitor the changes in gene expression at the transcriptional level in barley leaves during the reproductive stage under drought conditions, the 22K Affymetrix Barley 1 microarray was used to screen two drought-tolerant barley genotypes, Martin and Hordeum spontaneum 41-1 (HS41-1), and one drought-sensitive genotype Moroc9-75. Seventeen genes were expressed exclusively in the two drought-tolerant genotypes under drought stress, and their encoded proteins may play significant roles in enhancing drought tolerance through controlling stomatal closure via carbon metabolism (NADP malic enzyme, NADP-ME, and pyruvate dehydrogenase, PDH), synthesizing the osmoprotectant glycine-betaine (C-4 sterol methyl oxidase, CSMO), generating protectants against reactive-oxygen-species scavenging (aldehyde dehydrogenase,ALDH, ascorbate-dependent oxidoreductase, ADOR), and stabilizing membranes and proteins (heat-shock protein 17.8, HSP17.8, and dehydrin 3, DHN3). Moreover, 17 genes were abundantly expressed in Martin and HS41-1 compared with Moroc9-75 under both drought and control conditions. These genes were possibly constitutively expressed in drought-tolerant genotypes. Among them, seven known annotated genes might enhance drought tolerance through signalling [such as calcium-dependent protein kinase (CDPK) and membrane steroid binding protein (MSBP)], anti-senescence (G2 pea dark accumulated protein, GDA2), and detoxification (glutathione S-transferase, GST) pathways. In addition, 18 genes, including those encoding Δl-pyrroline-5-carboxylate synthetase (P5CS), protein phosphatase 2C-like protein (PP2C), and several chaperones, were differentially expressed in all genotypes under drought; thus they were more likely to be general drought-responsive genes in barley. These results could provide new insights into further understanding of drought-tolerance mechanisms in barley.

Variation in Fusarium graminearum and cultivar resistance to wheat scab

Understanding variation in pathogen virulence and cultivar resistance is important for development of effective strategies for breeding wheat cultivars resistant to scab. Six isolates of Fusarium graminearum from China and the United States were compared for variation in cultural characteristics and virulence on nine wheat cultivars with different degrees of resistance to scab. The isolates varied in their cultural characteristics and ability to cause scab, but there was no consistent specificity of cultivar resistance or pathogen virulence. Therefore, a mixture of local isolates is an appropriate inoculum to screen for scab resistance. Subculturing the fungus on potato dextrose agar for eight generations did not reduce virulence. In the greenhouse, eight cultivars were tested five times over 3 years by inoculating one central floret in a spike with an Indiana isolate of the fungus. Cultivars Ning 7840, Sumai 49, Fu 5114, and Sumai 3 were consistently resistant. The fungus spread from the inoculated spikelet to noninoculated spikelets of resistant cultivars in less than 20% of the plants, and spread was not evident until 12 days after inoculation. All plants of susceptible cultivar Clark showed spread of infection, and symptoms appeared on noninoculated spikelets by 8 days after inoculation. Sudden blight on the top part of the spike may be an important characteristic of highly susceptible cultivars. Measurement of spread of scab within a spike is a stable and reliable estimate of cultivar resistance.

Amplified Fragment Length Polymorphism Markers Linked to a Major Quantitative Trait Locus Controlling Scab Resistance in Wheat

ABSTRACT Scab is a destructive disease of wheat. To accelerate development of scab-resistant wheat cultivars, molecular markers linked to scab resistance genes have been identified by using recombinant inbred lines (RILs) derived by single-seed descent from a cross between the resistant wheat cultivar Ning 7840 (resistant to spread of scab within the spike) and the susceptible cultivar Clark. In the greenhouse, F(5), F(6), F(7), and F(10) families were evaluated for resistance to spread of scab within a spike by injecting about 1,000 conidiospores of Fusarium graminearum into a central spikelet. Inoculated plants were kept in moist chambers for 3 days to promote initial infection and then transferred to greenhouse benches. Scab symptoms were evaluated four times (3, 9, 15, and 21 days after inoculation). The frequency distribution of scab severity indicated that resistance to spread of scab within a spike was controlled by a few major genes. DNA was isolated from both parents and F(9) plants of the 133 RILs. A total of 300 combinations of amplified fragment length polymorphism (AFLP) primers were screened for polymorphisms using bulked segregant analysis. Twenty pairs of primers revealed at least one polymorphic band between the two contrasting bulks. The segregation of each of these bands was evaluated in the 133 RILs. Eleven AFLP markers showed significant association with scab resistance, and an individual marker explained up to 53% of the total variation (R(2)). The markers with high R(2) values mapped to a single linkage group. By interval analysis, one major quantitative trait locus for scab resistance explaining up to 60% of the genetic variation for scab resistance was identified. Some of the AFLP markers may be useful in marker-assisted breeding to improve resistance to scab in wheat.

Parallel domestication of the Shattering1 genes in cereals

A key step during crop domestication is the loss of seed shattering. Here, we show that seed shattering in sorghum is controlled by a single gene, Shattering1 (Sh1), which encodes a YABBY transcription factor. Domesticated sorghums harbor three different mutations at the Sh1 locus. Variants at regulatory sites in the promoter and intronic regions lead to a low level of expression, a 2.2-kb deletion causes a truncated transcript that lacks exons 2 and 3, and a GT-to-GG splice-site variant in the intron 4 results in removal of the exon 4. The distributions of these non-shattering haplotypes among sorghum landraces suggest three independent origins. The function of the rice ortholog (OsSh1) was subsequently validated with a shattering-resistant mutant, and two maize orthologs (ZmSh1-1 and ZmSh1-5.1+ZmSh1-5.2) were verified with a large mapping population. Our results indicate that Sh1 genes for seed shattering were under parallel selection during sorghum, rice and maize domestication.

Mapping QTLs for root traits in a recombinant inbred population from two indica ecotypes in rice

Abstract Evaluation of root traits in rainfed lowland rice is very difficult. Molecular genetic markers could be used as an alternative strategy to phenotypic selection for the improvement of rice root traits. This research was undertaken to map QTLs associated with five root traits using RFLP and AFLP markers. Recombinant inbred lines (RILs) were developed from two indica parents, IR58821–23-B-1–2-1 and IR52561-UBN-1–1-2, that were adapted to rainfed lowland production systems. Using wax-petrolatum layers to simulate a hardpan in the soil, 166 RILs were evaluated for total root number (TRN), penetrated root number (PRN), root penetration index (RPI, the ratio of PRN to TRN), penetrated root thickness (PRT) and penetrated root length (PRL) under greenhouse conditions during the summer and the fall of 1997. A genetic linkage map of 2022 cM length was constructed comprising 303 AFLP and 96 RFLP markers with an average marker space of 5.0 cM. QTL analysis via interval mapping detected 28 QTLs for these five root traits, which were located on chromosomes 1, 2, 3, 4, 6, 7, 10 and 11. Individual QTLs accounted for between 6 and 27% of the phenotypic variation. Most of the favorable alleles were derived from the parent IR58821–23-B-1–2-1, which was phenotypically superior in root traits related to drought resistance. Three out of six QTLs for RPI were detected in both summer and fall experiments and they also were associated with PRN in both experiments. Out of eight QTLs for RPT, five were common in both seasons. Two genomic regions on chromosome 2 were associated with three root traits (PRN, PRT and RPI), whereas three genomic regions on chromosomes 2 and 3 were associated with two root traits (PRT and RPI). Two QTLs affecting RPI and two QTLs affecting PRT were also found in similar genomic regions in other rice populations. The consistent QTLs across genetic backgrounds and the common QTLs detected in both experiments should be good candidates for marker-assisted selection toward the incorporation of root traits in a drought resistance breeding program, especially for rainfed lowland rice.

Inheritance of resistance to Fusarium graminearum in wheat.

Abstract To study the inheritance of resistance in wheat to Fusarium graminearum, six resistant cultivars from China were crossed to two susceptible cultivars. The parents and their progenies were evaluated in the greenhouse for resistance to the spread of scab within a spike. A central floret was inoculated by injecting a droplet of inoculum at the time of anthesis. Inoculated plants were kept in a moist chamber for three subsequent nights. The proportion of scabbed spikelets was recorded six-times from 3-days to 21-days after inoculation, and the area under the disease progress curve (AUDPC) was calculated from these proportions. One to three genes, depending on the cultivar, conditioned resistance to scab as reflected by the AUDPC. A simple additive-dominance effect model fitted the segregation data for 8 of the 11 crosses. Dominance and epistatic effects were significant in a few crosses. These effects increased resistance in some crosses but decreased resistance in others. However, relative to additive effects, dominant and epistatic effects accounted for only a small portion of the genetic effects in the populations evaluated. The importance of additive effects means that it should be possible to accumulate different genes to enhance resistance to scab in wheat.

Genic and nongenic contributions to natural variation of quantitative traits in maize

The complex genomes of many economically important crops present tremendous challenges to understand the genetic control of many quantitative traits with great importance in crop production, adaptation, and evolution. Advances in genomic technology need to be integrated with strategic genetic design and novel perspectives to break new ground. Complementary to individual-gene-targeted research, which remains challenging, a global assessment of the genomic distribution of trait-associated SNPs (TASs) discovered from genome scans of quantitative traits can provide insights into the genetic architecture and contribute to the design of future studies. Here we report the first systematic tabulation of the relative contribution of different genomic regions to quantitative trait variation in maize. We found that TASs were enriched in the nongenic regions, particularly within a 5-kb window upstream of genes, which highlights the importance of polymorphisms regulating gene expression in shaping the natural variation. Consistent with these findings, TASs collectively explained 44%-59% of the total phenotypic variation across maize quantitative traits, and on average, 79% of the explained variation could be attributed to TASs located in genes or within 5 kb upstream of genes, which together comprise only 13% of the genome. Our findings suggest that efficient, cost-effective genome-wide association studies (GWAS) in species with complex genomes can focus on genic and promoter regions.

Molecular mapping of a quantitative trait locus for aluminum tolerance in wheat cultivar Atlas 66

Genetic improvement of aluminum (Al) tolerance is one of the cost-effective solutions to improve wheat (Triticum aestivum) productivity in acidic soils. The objectives of the present study were to identify quantitative trait loci (QTL) for Al-tolerance and associated PCR-based markers for marker-assisted breeding utilizing cultivar Atlas 66. A population of recombinant inbred lines (RILs) from the cross Atlas 66/Century was screened for Al-tolerance by measuring root-growth rate during Al treatment in hydroponics and root response to hematoxylin stain of Al treatment. After 797 pairs of SSR primers were screened for polymorphisms between the parents, 131 pairs were selected for bulk segregant analysis (BSA). A QTL analysis based on SSR markers revealed one QTL on the distal region of chromosome arm 4DL where a malate transporter gene was mapped. This major QTL accounted for nearly 50% of the phenotypic variation for Al-tolerance. The SSR markers Xgdm125 and Xwmc331 were the flanking markers for the QTL and have the potential to be used for high-throughput, marker-assisted selection in wheat-breeding programs.