On the cover

Carrots are among the top-ten most economically important vegetable crops in the world. However, the gene pool of cultivated carrots is narrow, and the collection and preservation of carrot germplasm are very limited in China. A number of mutant lines induced by EMS showing inheritable morphological mutations were obtained such as leaf shape (A: Wild type, B, C: Mutants), leaf color (D: Wild type, E–K: Mutants) and taproot color (L: Wild type, M–O: Mutants). These mutants can not only enrich the carrot germplasm, but also provide resources for the functional study of carrot genes (This issue, p. 540–546).

(Z. Wu: Shanxi Agricultural University)

Thinopyrum intermedium (2n = 6x = 42, E₁E₁E₂E₂XX) serves as an important gene source of desirable traits for genetic improvement of wheat cultivars resistant to stresses. This study used the comparative proteomic approach to identify stress defense related proteins in the developing grains of common wheat (Zhongmai 8601)-Thinopyron intermedium 7XL/7DS translocation line YW642 and to explore their potential values for improving wheat stress resistance. Two-dimensional electrophoresis identified 124 differentially accumulated protein spots representing 100 unique proteins, which mainly participated in stress defense, energy metabolism, protein metabolism and folding and storage protein synthesis. Among these, 16 were unique and 35 were upregulated in YW642. The upregulated DAPs were mainly involved in biotic and abiotic stress defense. Further cis-elements analysis of these stress-related DAP genes revealed that phytohormone responsive elements such as ABREs, G-box, CGTCA-motif and TGACG-motif, and environment responsive element As-1 were particularly abundant, which could play important roles in response to various stressors. Transcription expression analysis by RNA-seq and qRT-PCR demonstrated a large part of the stress-related DAP genes showed an upregulated expression in the early-to-middle stages of grain development. Our results proved that Thinopyron intermedium contains abundant stress responsive proteins that have potential values for the genetic improvement of wheat stress resistance.

The mass scattering of basidiospores during the cultivation of edible mushrooms causes serious problems, such as allergic reactions in workers. Sporulation-deficient (sporeless) cultivars would be very useful for preventing these issues. We aimed to identify the single-nucleotide polymorphism (SNP) that is responsible for the single dominant sporeless mutation of the Tamogitake 108Y2D mutant using next-generation sequencing (NGS) and TILLING technology and to develop an allele-specific PCR marker for sporeless breeding. By comparing the sequences of the wild-type and its mutant genomes, we identified 685 mutation loci in gene regions and pinpointed one SNP only consistent with sporeless phenotype for 105 segregants, i.e., a C to T located at position 1,950 of the exonic region of a putative fungal transcription factor that generated a stop codon. We developed an allele-specific marker based on the identified SNP, and its high practicality was validated using tests against progenies from several hybrids and wild isolates from different geographical origins. Thus, the allele-specific PCR marker developed here will be useful for marker-assisted selection in the breeding of the sporeless trait of this mushroom. Furthermore, the technical success of SNP identification and marker development based on NGS genome data can help achieve efficient mutation breeding in mushrooms.

Carrot is among the top-ten most economically important vegetable crops in the world. However, the gene pool of cultivated carrot is narrow and the collection and preservation of carrot germplasm are very limited in China. In this study, seeds of carrot inbred line “17005” were treated by ethyl methyl sulfone (EMS) to construct a mutant library. The conditions of EMS mutagenesis on inbred line “17005” were optimized, including treatment of seeds at 0.5% EMS for 6 h. We obtained a number of mutant lines showing inheritable morphological mutations in cotyledon, growth point, leaf, taproot in the vegetative phase and mutations in bolting time, primary stem height and color, secondary branch, flower and seed in the reproductive phase through M₂ and M₃. The F₂ segregating population from the cross of yellow taproot and purple-red epidermis taproot with wild type showed that these two mutants were controlled by single recessive gene respectively. The inheritable mutants can not only enrich the carrot germplasm, but also provide resources for the function research of carrot gene.

Walnut is an important cultivated tree with high economic value and wide distribution across China. The objective was to breed a new walnut cultivar with high yield and desirable nut and tree qualities that could meet the demands of the walnut industry in China. ‘Liaoning 4’ walnut cultivar is lateral bearing which originated from a controlled cross between the Persian walnut (J. regia) selections ‘Liaoning Chaoyang big and rough walnut’ and ‘11001’. During long term assessment and research, ‘Liaoning 4’ walnut performed well and it was released as a new cultivar in China on 15 Oct. 2018. It has a high yield and excellent nut traits and has thus been widely planted in North China.

Paw San Hmwe (PSH) is a high-quality rice cultivar from Myanmar. PSH has short and broad grains, but the grains become slender after cooking. This desirable feature can be described as a high value of grain length-breadth relative expansion index (GREI). To understand the genetic basis of high GREI in PSH, we crossed PSH with Guang 8B (G8B), a rice cultivar from China with low GREI, to develop an F₂ population and a subsequent F_2:3 population. Based on the phenotypes of these two populations measured in two years and using the method of sequencing-based bulked segregant analysis followed by verification with conventional linkage-based QTL mapping method, we mapped three QTLs for GREI. The three QTLs were located on chromosomes 3, 5 and 12, respectively, with the trait-increasing alleles all from PSH, and could explain a total of 62.5% of the phenotypic variance and 84.1% of the additive genetic variance. The results suggest that the three QTLs would be useful for the genetic improvement of GREI in rice, and the linked markers will facilitate the selection of the favorable alleles from PSH in breeding.

Agricultural expansion requires the deployment of stress-tolerant crops like safflower (Carthamus tinctorius L.). In safflower breeding, oil improvement in early generations requires indirect selection through simply inherited traits. The oil quality is mostly related to the fatty acid profile, which is determined by the OL locus. The aim of this research was to identify simple easy-to-measure traits that indirectly explain oil content variation and its interaction with yield components, and also to generate an effective tool for genotyping the OL locus. A field experiment with F₅ and pure lines was carried out to correlate the oil content with 18 traits including yield components, and phenological and morphological characteristics. KASP technology using primers designed according to the ctFAD2-1 gene sequence was applied for OL locus genotyping and validated through fatty acids phenotyping. Hull content, the length:width ratio of the grain, and plant height were identified as the most promising selection tools for increasing oil content, and grains per capitulum was the best yield component for increasing yield without decreasing the oil content. KASP genotyping successfully worked as a MAS tool, identifying oleic and linoleic genotypes. These tools enhance options for improving oil content and quality for safflower breeding.

To find new QTLs responsible for kernel cracking resistance, we screened 50 CSSLs derived from the moderately resistant cultivar ‘Itadaki’ (O. sativa L.) and the donor O. rufipogon. Two lines, IRSL 30 and IRSL 37, were selected as resistant. QTL analyses of the percentage of cracked kernels (PCK) in F₄ individuals derived from “Itadaki/IRSL 30” and “Itadaki/IRSL 37” identified a major QTL, qCR (Cracking Resistance) 8-2, at the same position on chromosome 8 in both populations. ‘IRSL 30’ and ‘IRSL 37’ had a reduced PCK. These results show that qCR8-2 is likely to be an important QTL for kernel cracking resistance. Both lines had long awns, linked to qCR8-2, but the awnless line ‘Chukei 19301’ was also derived from “Itadaki/IRSL 37”, so qCR8-2 is distinct from the gene for awn development. We consider that qCR8-2 will help in the breeding of new rice cultivars with high cracking resistance and in elucidating the physiological mechanism of kernel cracking.

Genetic variations of 179 rice (Oryza sativa L.) accessions from Cambodia were clarified based on the analyses for heading date, chromosome components, and blast resistance. The dominant accessions were found in three regions; early heading in North East (NE), medium in Central (CT), and late in South East (SE) along the Mekong River in the investigation at Ishigaki, Japan. In contrast, wide variations were observed in two regions, South West (SW) and North West (NW) located around Tonle Sap Lake. Polymorphism data of SSR markers showed that accessions were classified into Japonica Group (cluster Ib), and Indica Groups (IIa and IIb). In the NW and SW, the accessions of all three clusters were found, but these accessions in NE, CT, and SE, were limited to one or two clusters. Accessions were classified again into two clusters, A1 as having high resistance and A2 as having moderate resistance. Remarkable differences of these frequencies of clusters, A1 and A2, were found in the SE, SW, and NW, and similar with these of the whole accessions were in NE and CT. Rice accessions varied among the five regions, and there was a dramatic difference between the regions along Mekong River and the regions around Tonle Sap Lake.

Camellia oleifera Abel. (C. oleifera) is a cultivable plant with important economic value. It is very helpful for the scientific utilization, cultivation and preservation of germplasm resources through evaluating the genetic diversity. In this study, we estimated the genetic relationship of 150 accessions of C. oleifera using morphological and economic traits, as well as SSR molecular marker. Through the variation and cluster analysis of 17 morphological and economic traits, the germplasm was divided into a candidate core breeding group with higher economic traits and a core breeding group with higher morphological traits. The genetic similarity coefficients of SSR markers ranged from 0.05 to 0.91, and the germplasm materials were divided into five groups. The results demonstrated that C. oleifera germplasms perform a rich genetic variation. This is the first report to evaluate the genetic diversity of different C. oleifera germplasms using the morphological and economic traits, together with SSR molecular marker, and the results allow us to find evidence for the origin of varieties, establish core breeding populations and its fingerprint.

Genomic selection (GS) is being increasingly employed in plant breeding programs to accelerate genetic gain of economically important traits. However, its efficiency differs greatly across species, due to differences in reproduction and breeding strategies. Onion (Allium cepa L.) is an out-crossing crop but can be easily self-pollinated. High inbreeding depression occurs, and contamination of self-pollinated seeds is unavoidable in onion breeding. Taking this into consideration, 10-year breeding programs with and without GS were simulated. In addition to general GS, we proposed GS schemes to prevent inbreeding depression by avoiding co-selection of close relatives and combining the shortening of generation time and updating of the prediction model. The results showed that general GS with shortening of generation time yielded the highest genetic gain among the selection schemes in early years. However, inbreeding increased rapidly, reaching very high levels in later years. The proposed GS combining shortening of generation time with updating of the prediction model was superior to the others in later years, as it yielded relatively high genetic gain while maintaining significantly low levels of inbreeding. These results suggested that GS can be beneficial in onion breeding, and an optimal scheme should be selected depending on the selection period.

Non-additive (dominance and epistasis) effects have remarkable influences on hybrid performance, e.g., via heterosis. Nevertheless, only additive effects are often considered in genomic predictions (GP). In this study, we demonstrated the importance of dominance effects in the prediction of hybrid performance in bioenergy sorghum [Sorghum bicolor (L.) Moench]. The dataset contained more than 400 hybrids between 200 inbred lines and two testers. The hybrids exhibited considerable heterosis in culm length and fresh weight, and the degree of heterosis was consistent with the genetic distance from the corresponding tester. The degree of heterosis was further different among subpopulations. Conversely, Brix exhibited limited heterosis. Regarding GP, we examined three statistical models and four training dataset types. In most of the dataset types, genomic best linear unbiased prediction (GBLUP) with additive effects had lower prediction accuracy than GBLUP with additive and dominance effects (GBLUP-AD) and Gaussian kernel regression (GK). The superiority of GBLUP-AD and GK depended on the level of dominance variance, which was high for culm length and fresh weight, and low for Brix. Considering subpopulations, the influence of dominance was more complex. Our findings highlight the importance of considering dominance effects in GP models for sorghum hybrid breeding.

Soil-borne wheat mosaic virus (SBWMV), a ubiquitous pathogen commonly encountered in temperate regions of the Northern hemisphere, can damage a number of economically important cereal crops, notably wheat and barley. Given that the plasmodiophorid cercozoan Polymyxa graminis, which acts as the vector of SBWMV, can survive in the soil for many decades, the only feasible control measure is the deployment of resistant cultivars. Here, a quantitative trait locus (QTL) approach was taken to characterize the genetic basis of the SBWMV resistance exhibited by the barley cultivar Haruna Nijo. The analysis revealed that between 33% and 41% of the variation for the measure chosen to represent resistance was under the control of a gene(s) mapping to a region at the distal end of the short arm of chromosome 2H. In contrast to most of the genes known to encode resistance to soil-borne mosaic viruses, the allele specifying resistance was dominant over those present in a susceptible genotype.

We developed a new cultivar of Tartary buckwheat (Fagopyrum tataricum Gaertn.), ‘Darumadattan’. This is the first semidwarf Tartary buckwheat cultivar to be developed by mutation breeding using gamma-ray irradiation. In 1999, 100 dry seeds of the leading Japanese cultivar, ‘Hokkai T8’ (known at that time as ‘Hokkei 1’), were gamma-ray-irradiated with a total dose of 500 Gy (25 Gy/h × 20 h) at the Institute of Radiation Breeding (IRB), National Institute of Agrobiological Sciences, Hitachiomiya, Ibaraki, Japan. The seeds were sown in August 1999 in a field at IRB, and M₂ seeds were collected from the eight individual plants that survived. In August 2000, 240 M₂ seeds were sown in a field, and one semidwarf plant was found. The line named ‘IRBFT-20’ developed from the selected plant was investigated for its semidwarf characteristic and genetic stability in 2001–2005. ‘IRBFT-20’ was submitted for registration in 2011 and registered as the cultivar ‘Darumadattan’ in 2013. This name was chosen because the plants resemble “Daruma dolls” and “dattan” means “Tartary” in Japanese. ‘Darumadattan’ is a highly lodging-resistant and high-yielding cultivar and is expected to be used as both a commercial cultivar and a crossing parent.

Cadmium (Cd) is a toxic heavy metal that is mainly accumulated through the consumption of foods produced in Cd-contaminated fields. Phytoremediation is one of the most effective methods to reduce the soil Cd concentration. In this study, we bred a new rice line, ‘Akita 119’, for Cd phytoremediation. ‘Akita 119’ was obtained by a soft X-ray mutation of ‘Cho-ko-koku’, a naturally high-Cd-accumulating rice cultivar. The heading date of ‘Akita 119’ was about 2 weeks later than that of ‘Akitakomachi’, which is the leading cultivar in Akita Prefecture, Japan. ‘Akita 119’ has a short culm length and many panicles. The shattering resistance and lodging resistance of ‘Akita 119’ were improved compared to ‘Cho-ko-koku’. The thousand-grain weight of ‘Akita 119’ was much smaller than that of ‘Akitakomachi’, and grains of ‘Akita 119’ could be easily distinguished from general japonica cultivars. When ‘Akita 119’ was grown in Cd-contaminated fields, the shoot dry weight and Cd concentration were similar to those of ‘Cho-ko-koku’. These results demonstrate that ‘Akita 119’ has improved agronomic characteristics compared to ‘Cho-ko-koku’ while retaining the ability to extract Cd. Therefore, it should be considered a promising candidate for Cd phytoremediation in paddy fields in northern parts of Japan.

In addition to Ogura cytoplasmic male sterility (CMS), which is used extensively for F₁ hybrid seed production in Brassicaceae crops, two other CMS systems, NWB CMS and DCGMS, have also been identified. The causal gene for the latter two CMS systems has been identified as a novel chimeric gene, orf463. We previously reported that orf463 is specific to black radish cultivars and that it is present in line ‘RS-5’ of Raphanus raphanistrum; however, the orf463 sequence in ‘RS-5’ differed from that of black radish cultivars. Though, R. raphanistrum with an orf463 sequence identical to that found in black radish cultivars was recently identified. We therefore sought to determine whether the orf463 gene in line ‘RS-5’ induces CMS in radishes. We crossed ‘RS-5’ as a female parent with a cultivated radish, ‘Uchiki-Gensuke’, as a male parent, and examined the gross plant morphology and pollen fertility of the resulting progeny. The F₂ population contained both male sterile plants and plants with black roots. The findings showed that R. raphanistrum contains two types of orf463 genes that induce CMS, and that the origin of black radishes could be attributed to R. raphanistrum having orf463 gene.