Exploiting selective genotyping to study genetic diversity of resistance to Fusarium head blight in barley

Bringing Barley Back: Analysis of Heritage Varieties for Use as Germplasm Sources to Improve Resistance against the Most Devastating, Contemporary Disease in Canada, Fusarium Head Blight (Fusarium graminearum)

Fusarium head blight (FHB), caused by Fusarium graminearum, is currently the most devastating disease for barley (Hordeum vulgare) in Canada. Associated mycotoxins can compromise grain quality, where deoxynivalenol (DON) is considered particularly damaging due to its frequency of detection. Breeding barley with a lower DON content is difficult, due to the poor adaptation and malt quality of resistance sources. A set of European-derived heritage varieties were screened in an FHB nursery in Charlottetown, PE, with selections tested at Brandon, MB, between 2018-2022. Genetic evaluation demonstrated a distinct clustering of Canadian varieties from the heritage set. At Brandon, 72% of the heritage varieties ranked lower for DON content than did the moderately resistant Canadian check 'AAC Goldman', but resistance was associated with later heading and taller stature. In contrast with Canadian modern malting variety 'AAC Synergy', general deficiencies were observed in yield, enzyme activity, and extract, along with higher protein content. Nonetheless, several resistant varieties were identified with reasonable a heading date and yield, including 'Chevallier Chile', 'Domen', 'Djugay', 'Hannchen', 'Heils Franken', 'Moravian Barley', 'Loosdorfer' with 'Golden Melon', 'Nutans Moskva', and 'Vellavia', these being some of the most promising varieties when malting quality characteristics were also considered. These heritage resources could be used as parents in breeding to develop FHB-resistant malting barley varieties.

Interactions Among Multiple Quantitative Trait Loci Underlie Rhizome Development of Perennial Rice

Perennial crops have some advantages over annuals in soil erosion prevention, lower labor and water requirements, carbon sequestration, and maintenance of thriving soil ecosystems. Rhizome, a kind of root-like underground stem, is a critical component of perenniality, which allows many grass species to survive through harsh environment. Identification of rhizome-regulating genes will contribute to the development of perennial crops. There have been no reports on the cloning of such genes until now, which bring urgency for identification of genes controlling rhizomatousness. Using rhizomatous Oryza longistaminata and rhizome-free cultivated rice as male and female parents, respectively, genetic populations were developed to identify genes regulating rhizome. Both entire population genotyping and selective genotyping mapping methods were adopted to detect rhizome-regulating quantitative trait loci (QTL) in 4 years. Results showed that multiple genes regulated development of rhizomes, with over 10 loci related to rhizome growth. At last, five major-effect loci were identified including qRED1.2, qRED3.1, qRED3.3, qRED4.1, and qRED4.2. It has been found that the individual plant with well-developed rhizomes carried at least three major-effect loci and a certain number of minor-effect loci. Both major-effect and minor-effect loci worked together to control rhizome growth, while no one could work alone. These results will provide new understanding of genetic regulation on rhizome growth and reference to the subsequent gene isolation in rice. And the related research methods and results in this study will contribute to the research on rhizome of other species.

Molecular mapping of major QTL conferring resistance to orange wheat blossom midge (Sitodiplosis mosellana) in Chinese wheat varieties with selective populations

Two novel midge resistance QTL were mapped to a 4.9-Mb interval on chromosome arm 4AL based on the genetic maps constructed with SNP markers. Orange wheat blossom midge (OWBM) is a devastating insect pest affecting wheat production. In order to detect OWBM resistance genes and quantitative trait loci (QTL) for wheat breeding, two recombinant inbred line (RIL) populations were established and used for molecular mapping. A total of seven QTL were detected on chromosomes 2D, 4A, 4D and 7D, respectively, of which positive alleles were all from the resistant parents except for the QTL on 7D. Two stable QTL (QSm.hbau-4A.2-1 and QSm.hbau-4A.2-2) were detected in both populations with the LOD scores ranging from 5.58 to 29.22 under all three environments, and they explained a combined phenotypic variation of 24.4-44.8%. These two novel QTL were mapped to a 4.9-Mb physical interval. The single-nucleotide polymorphism (SNP) markers AX-109543456, AX-108942696 and AX-110928325 were closely linked to the QTL and could be used for marker-assisted selection (MAS) for OWBM resistance in wheat breeding programs.

Association Analysis for Bacterial Spot Resistance in a Directionally Selected Complex Breeding Population of Tomato

Bacterial spot of tomato is caused by at least four species of Xanthomonas with multiple physiological races. We developed a complex breeding population for simultaneous discovery of marker-trait linkage, validation of existing quantitative trait loci (QTL), and pyramiding of resistance. Six advanced accessions with resistance from distinct sources were crossed in all combinations and their F1 hybrids were intercrossed. Over 1,100 segregating progeny were evaluated in the field following inoculation with X. euvesicatoria race T1 strains. We selected 5% of the most resistant and 5% of the most susceptible progeny for evaluation as plots in two subsequent replicated field trials inoculated with T1 and T3 (X. perforans) strains. The estimated heritability of T1 resistance was 0.32. In order to detect previously reported resistance genes, as well as novel QTL, we explored methods to correct for population structure and analysis based on single markers or haplotypes. Both single-point and haplotype analyses identified strong associations in the genomic regions known to carry Rx-3 (chromosome 5) and Rx-4/Xv3 (chromosome 11). Accounting for kinship and structure generally improved the fit of statistical models. Detection of known loci was improved by adding kinship or a combination of kinship and structure using a Q matrix from model-based clustering. Additional QTL were detected on chromosomes 1, 4, 6, and 7 for T1 resistance and chromosomes 2, 4, and 6 for T3 resistance (P < 0.01). Haplotype analysis improved our ability to trace the origin of positive alleles. These results demonstrate that both known and novel associations can be identified using complex breeding populations that have experienced directional selection.

Haplotype diversity and population structure in cultivated and wild barley evaluated for Fusarium head blight responses

Fusarium head blight (FHB) is a threat to barley (Hordeum vulgare L.) production in many parts of the world. A number of barley accessions with partial resistance have been reported and used in mapping experiments to identify quantitative trait loci (QTL) associated with FHB resistance. Here, we present a set of barley germplasm that exhibits FHB resistance identified through screening a global collection of 23,255 wild (Hordeum vulgare ssp. spontaneum) and cultivated (Hordeum vulgare ssp. vulgare) accessions. Seventy-eight accessions were classified as resistant or moderately resistant. The collection of FHB resistant accessions consists of 5, 27, 46 of winter, wild and spring barley, respectively. The population structure and genetic relationships of the germplasm were investigated with 1,727 Diversity Array Technology (DArT) markers. Multiple clustering analyses suggest the presence of four subpopulations. Within cultivated barley, substructure is largely centered on spike morphology and growth habit. Analysis of molecular variance indicated highly significant genetic variance among clusters and within clusters, suggesting that the FHB resistant sources have broad genetic diversity. The haplotype diversity was characterized with DArT markers associated with the four FHB QTLs on chromosome 2H bin8, 10 and 13 and 6H bin7. In general, the wild barley accessions had distinct haplotypes from those of cultivated barley. The haplotype of the resistant source Chevron was the most prevalent in all four QTL regions, followed by those of the resistant sources Fredrickson and CIho4196. These resistant QTL haplotypes were rare in the susceptible cultivars and accessions grown in the upper Midwest USA. Some two- and six-rowed accessions were identified with high FHB resistance, but contained distinct haplotypes at FHB QTLs from known resistance sources. These germplasm warrant further genetic studies and possible incorporation into barley breeding programs.

Three EST-SSR markers associated with QTL for the growth of the clam Meretrix meretrix revealed by selective genotyping

The clam Meretrix meretrix is a member of widely cultured, commercially important clams. A marker-trait association analysis was performed using expressed sequence tag (EST) simple sequence repeat (SSR) markers for marker-assisted selection in M. meretrix. Three markers, MM1272, MM2034, and MM7721, were found to be significantly associated with quantitative trait loci (QTLs) controlling shell length (P < 0.0001) in clams of a fast-growing population (JSF) and a control population (JSC). The 144-bp allele of MM1272, the 154-bp allele of MM2034, and the 152- and 165-bp alleles of MM7721 showed a significantly higher frequency in the JSF population (17.65, 36.41, 28.67, and 29.33 %) than in the JSC population (4.65, 8.33, 3.47, and 5.56 %). The three markers showed lower values for the number of alleles and observed heterozygosity as well as a higher proportion of homozygotes in JSF than in JSC population. The three markers have been further confirmed in the high and low tails of another population (09G₃SPSB); similarly, lower values for the number of alleles and observed heterozygosity as well as a higher proportion of homozygotes were found in 09G₃SPSB(H). The putative functions of the three gene fragments containing MM1272, MM2034, and MM7721 also suggested that the three SSR-containing genes might be involved in growth of M. meretrix. All the results suggest that the three EST-SSR markers associated with growth QTLs would be useful for marker-assisted selection in M. meretrix breeding.

Detection of marker-QTL associations by studying change in marker frequencies with selection

The value of selective genotyping for the detection of QTL has already been studied from a theoretical point of view but with the assumption of a negligible contribution (r2P) of the QTL to the phenotypic variance. For predicting change in gene frequency, we show that this assumption is only valid for r2P less than 0.05 and for a proportion selected higher than 1%. Therefore, we develop a study of the optimization of selective genotyping without assumption on QTL effect, with selection either of both tails (bidirectional genotyping or BSG) or only one tail (unidirectional genotyping or USG). For a given population size of phenotyped plants the optimal proportion selected for selective genotyping is around 30% for each tail. For the same investment as in ANOVA, by investing more in phenotyping than in genotyping when the cost ratio of genotyping to phenotyping is higher than 1, the optimal proportion selected appears to be between 10 and 20% for each tail. It is mainly affected by the cost ratio and decreases when the cost ratio increases. At this optimum, BSG is competitive with ANOVA, or even more powerful, when the cost ratio is higher than 1. USG can also be competitive when the cost ratio is higher than 2. Using experimental data from two populations of about 300 F4 inbred families of maize, it was verified that BSG at the optimum gives the same results as ANOVA or is better whereas USG is less powerful or equivalent.

Genomic regions involved in response to grain yield selection at high and low nitrogen fertilization in maize

In order to validate the role of genomic regions involved in nitrogen use efficiency and detected in a population of recombinant inbred lines (RIL), we have applied from the same population a recurrent selection for adaptation to low N-input (N0) and to high N-input (N1). Variation of allele frequency at neutral marker during the two cycles of recurrent selection may provide information about markers linked to QTLs. Significant temporal variation of allele frequency was investigated using the test of Waples, which tests the hypothesis of genetic drift versus selection. Most genomic regions (12/19) responding to selection were detected for selection at high N-input and only two were common to selection at high and low N-inputs. This was consistent with the greater grain yield response to selection observed for the population selected under high N-input compared with the population selected under low N-input, when they were evaluated at high N-fertilization. In contrast, when they were evaluated at low N-input both types of selection gave similar yield. As was expected, in the first cycle we observed selection of markers linked to grain yield QTLs. In the course of the second cycle three situations were observed: the confirmation of most regions already selected in C1 including all C1 regions overlapping with grain yield QTLs; the non-confirmation of some C1 regions (2/9); and the identification of new genomic zones (10/17). The detected marker-QTL associations revealed the consistency of the involvement of some traits, such as root architecture and glutamine synthetase activity, which would be of major importance for grain yield setting whatever the nitrogen fertilization.