On the cover

Information on the genes determining grain shape and related traits is important for breeding Fagopyrum species. A seed shape similar to F. esculentum (common buckwheat) is considered desirable, as the current processing technology has been developed to suit common buckwheat seeds. F. tataricum Gaertn. has high nutritional value but needs improvement in the seed shape. Interspecific hybridization is a promising method to obtain seeds similar to common buckwheat, but a strong postzygotic barrier between F. tataricum and F. esculentum makes genetic exchange impossible. F. cymosum, which has a seed shape similar to F. esculentum, provides an additional source of the genetic polymorphisms needed to improve other buckwheat species. In this issue, the effects of interspecific hybridization in the genus Fagopyrum on seed traits are discussed. The photographs show the seed types of F. tataricum and F. cymosum: rice type (top left), round type (top right), notched type (bottom left) of F. tataricum, and F. cymosum (bottom right) (This issue, p. 232–237).

(Ivan N. Fesenko: Lab of Buckwheat Breeding, Federal Scientific Center of Grain Legumes and Groats Crops)

Clubroot, caused by Plasmodiophora brassicae is one of the most severe threats to brassica species in China and worldwide. Breeding for clubroot resistant varieties is one of the best ways to overcome this disease. In this study, we introduced clubroot resistance (CR) gene CRd from Chinese cabbage (85-74) into elite Brassica napus inbred line Zhongshuang 11 through interspecific hybridization and subsequent backcrossing with whole-genome molecular marker-assisted selection (MAS). The resistant test of CRd to P. brassicae isolates was evaluated in the greenhouse as well as in field conditions. Close linkage markers and the whole-chromosome background marker selection approach improved the recovery rate from 78.3% in BC₁ to 100% in BC₃F₁. The improved clubroot-resistant variety, Zhongshuang11R, was successfully selected in the BC₃F₂ generation. The greenhouse and field resistant tests revealed that Zhongshuang11R was resistant to P. brassicae pathotypes. The agronomic characteristics of Zhongshuang11R were similar to those of its recurrent parental line, including oil content, composition of fatty acid, plant height, primary effective branches, grain yield per plant and thousand-seed weight. In addition, the oil quality could satisfy the quality requirements for commercial rapeseed oil. Our results will enrich the resistant resources of canola and will certainly accelerate clubroot resistance breeding programs in B. napus.

Seed dormancy, a vital strategy for wild plant species to adapt to an unpredictable environment in their natural habitats, was eliminated from cereals during the domestication process. Intraspikelet differences in grain size and seed dormancy have been observed in wild emmer wheat. To elucidate the genetic variation of these intraspikelet differences and to determine their genetic control, grain weight ratio (first florets/second florets) (GWR), germination rate, and germination index (GI) were analyzed in 67 wild and 82 domesticated emmer wheat accessions, as well as F₁ hybrids, F₂ populations, and F₃–F₆ populations derived from reciprocal crosses between wild and domesticated lines. Only the grains on the first florets of two-grained spikelets in wild accessions had varying degrees of dormancy with GI ranging from 0 to 1, which positively correlated with their GWR. This implies that wild emmer populations comprised genotypes with varying degrees of dormancy, including nondormant genotypes. According to segregations observed in F₂ populations, the intraspikelet grain weight difference was controlled by two independently inherited loci. Furthermore, low-GWR populations with low or high GI values could be selected in F₅ and F₆ generations, implying that the major loci associated with dormancy might be independent of intraspikelet grain weight difference.

Psathyrostachys huashanica is a relative of wheat (Triticum aestivum L.) with many disease resistance genes that can be used to improve wheat disease resistance. In order to enrich the germplasm resources available in wheat genetics and breeding, we assessed Fusarium head blight (FHB) resistance in 45 interspecific derivatives between wheat and Psathyrostachys huashanica during two years from 2017–2018. Two interspecific derivatives comprising, H-34-8-2-6-1 and H-24-3-1-5-19-1 were identified as FHB resistant lines. These two lines were examined based on their morphology and cytogenetics, as well as by genomic in situ hybridization (GISH), fluorescence in situ hybridization (FISH), molecular markers, and 660K genotyping array to determine their genetic construction. The results confirmed H-34-8-2-6-1 as a wheat–P. huashanica 1Ns long arm ditelosomic addition line and H-24-3-1-5-19-1 as a wheat–P. huashanica 2Ns substitution line. Assessments of the agronomic traits showed that H-34-8-2-6 had significantly higher kernel number per spike and self-fertility rate than parent 7182. In addition, compared with 7182, H-24-3-1-5-19-1 had a much lower plant height while the other agronomic traits were relatively similar. The two new lines are valuable germplasm materials for breeding FHB resistance in wheat.

To explore the genetic resources that could be utilized to help improve root system architecture phenotypes in rice (Oryza sativa), we have conducted genome-wide association studies to investigate maximum root length and crown root number in 135 10-day-old Japanese rice accessions grown hydroponically. We identified a quantitative trait locus for crown root number at approximately 32.7 Mbp on chromosome 4 and designated it qNCR1 (quantitative trait locus for Number of Crown Root 1). A linkage disequilibrium map around qNCR1 suggested that three candidate genes are involved in crown root number: a cullin (LOC_Os04g55030), a gibberellin 20 oxidase 8 (LOC_Os04g55070), and a cyclic nucleotide-gated ion channel (LOC_Os04g55080). The combination of haplotypes for each gene was designated as a haploblock, and haploblocks 1, 2, and 3 were defined. Compared to haploblock 1, the accessions with haploblocks 2 and 3 had fewer crown roots; approximately 5% and 10% reductions in 10-day-old plants and 15% and 25% reductions in 42-day-old plants, respectively. A Japanese leading variety Koshihikari and its progenies harbored haploblock 3. Their crown root number could potentially be improved using haploblocks 1 and 2.

Compared to common buckwheat (F. esculentum), Tartary buckwheat (F. tataricum) is very polymorphic in the type of seeds, but a seed type which is typical for F. esculentum, i.e. triangular seeds with flat sides and clear ribs, has been not found among the polymorphism. However, such seed type is typical for wild species F. cymosum which produces fertile hybrids in crosses with F. tataricum. Embryo rescue based interspecific cross F. esculentum × F. cymosum allowed reveal functional allelism of the genes determining the similar morphs of these species’ seeds, i.e. the seed type resulted from mutation(s) at same gene. The gene can be assigned as TAN (triangular). Variation for the seed shell thickness among recessives for the TAN carrying about 12% of F. tataricum genome, together with the shell thickness of a seed from the F₁ hybrid F. esculentum × F. cymosum compared to ones of the parents, suggests there are some genes influencing seed shell thickness. Also, it was supported by analyses of seeds characteristics of Tartary-based forms with some share of F. cymosum genetic material. In addition, cross F. tataricum × F. cymosum looks like an effective tool to increase 1000-seed weight of Tartary buckwheat-based breeding material.

Low temperatures at the young microspore stage (YMS) decreases spikelet fertility and is a major limiting factor to rice production in temperate Australia. Low temperature tolerance is a difficult trait to phenotype, hence there is a strong desire for the identification of quantitative trait loci (QTL) for their use in marker-assisted selection (MAS). Association mapping was used in several breeding populations with a known source of low temperature tolerance, Norin PL8, to identify QTL for low temperature tolerance. A novel QTL for spikelet fertility was identified on chromosome 6, qYMCT6.1, in which the Australian variety, Kyeema, was the donor for increased fertility. Additional five genomics regions were identified that co-located with previously reported QTL, two of which have been previously cloned. Additionally, for the first time a QTL for spikelet fertility qYMCT10.1, has been shown to co-locate with the number of dehisced anthers qYMCTF10.1 which increases the shedding of pollen from the anthers. This study revealed one new QTL for low temperature tolerance at YMS in temperate japonica germplasm and identified an additional five previously reported. These QTL will be utilised for MAS in the Australian rice breeding program and may have merit for temperate breeding programs globally.

The Japanese domestic tobacco (Nicotiana tabacum L.) cultivar ‘Kokubu’ shows high powdery mildew resistance that is controlled by splice-site mutations of two MILDEW LOCUS O genes, NtMLO1 and NtMLO2. We investigated the existence of the same NtMLO1/2 splice mutations in the genomes of various tobacco varieties cultivated in Japan and other countries. In total, 14 Japanese domestic cultivars, which were mainly distributed in Kagoshima, had splice-site mutations in both NtMLO1 and NtMLO2. In addition, tobacco cultivars containing only the NtMLO1 splice-site mutation were found in various tobacco production areas in Japan, but no cultivars with only the NtMLO2 splice-site mutation were detected. Moreover, the NtMLO1 splice-site mutation was detected in native Asian, Oriental and cigar tobacco varieties. Consequently, we speculate that these powdery mildew-resistant tobacco cultivars were generated relative recently in the Kagoshima area when a spontaneous mutation occurred at the NtMLO2 splice site in a cultivar already containing the NtMLO1 splice-site mutation and that the NtMLO1 splice-site mutation occurred during the early period of tobacco seed dissemination from the Americas to Asia and Japan.

Wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) are widely cultivated temperate crops. In breeding programs with these crops in Japan, effective genomic-assisted selection was performed by selecting core marker sets from thousands of genome-wide amplicon sequencing markers. The core sets consist of 768 and 960 markers for barley and wheat, respectively. These markers are distributed evenly across the genomes and effectively detect widely distributed polymorphisms in the chromosomes. The core set utility was assessed using 1,032 barley and 1,798 wheat accessions across the country. Minor allele frequency and chromosomal distributions showed that the core sets could effectively capture polymorphisms across the entire genome, indicating that the core sets are applicable to highly-related advanced breeding materials. Using the core sets, we also assessed the trait value predictability. As observed via fivefold cross-validation, the prediction accuracies of six barley traits ranged from 0.56–0.74 and 0.62 on average, and the corresponding values for eight wheat traits ranged from 0.44–0.83 and 0.65 on average. These data indicate that the established core marker sets enable breeding processes to be accelerated in a cost-effective manner and provide a strong foundation for further research on genomic selection in crops.

Oryza AA-genome complex comprises five wild species, O. rufipogon, O. barthii, O. longistaminata, O. glumaepatula, and O. meridionalis. Evolutionary relationships among these five wild species have remained contentious and inconclusive. We found that intron 20 of PolA1, a single-copy nuclear gene, was short (S-type: 141–142 bp) in O. rufipogon, O. barthii, and O. glumaepatula, while long (L-type: ca. 1.5 kb) introns were apparent in O. longistaminata and O. meridionalis. Because Oryza species containing BB, CC, EE, FF, and GG genome showed L-type introns, the S-type intron was probably derived from the L-type intron by the deletion of a 1.4 kb fragment through intramolecular homologous recombination between two tandem TTTTGC repeats. Excluding the large deletion sequence, intron 20 sequence of O. barthii was identical to that of O. longistaminata. As more than 3,470 accessions of O. rufipogon and O. sativa also contained the same intron 20 sequence with O. longistaminata except for single T-nucleotide deletion, which was shared with O. glumaepatuala, the deletion of the T-nucleotide probably occurred in the L-type intron 20 of O. logistaminata. Deletions of a large 1.4 kb fragment and single T-nucleotide within the intron 20 of PolA1 gene were considered as useful DNA markers to study the evolutionary relationships among Oryza AA-genome species.