On the cover

In many yellow soybean cultivars grown in Japan, pigmentation is suppressed throughout the seed coat, including the hilum region (right). Fully pigmented seeds are sometimes produced by yellow soybean cultivars as a result of a spontaneous mutation from I to i (left). A candidate for the I allele was isolated and designated GmIRCHS. The causal DNA changes in the mutation are small or large deletions that involve GmIRCHS. Recently, the whole-genome sequence of the Japanese yellow soybean cultivar ‘Enrei’ has been released. Based on this, the unidentified large deletion regions in the mutants were investigated (This issue, p. 334–338).

(M. Senda: Faculty of Agriculture and Life Science, Hirosaki University)

Salt tolerance has been an important issue in agriculture. Many genes involved in salt stress have been identified, but this knowledge has not led to development of a salt-tolerant crop that are practically useful. Despite hundreds of transgenic plants have been tested, there are few examples that demonstrated yield performance that are practically applicable to salt-affected fields. It is therefore important to figure out which genes should be targeted for artificial manipulation. However, given there are >500 of genes involved, it is almost impossible to test all the possible combinations of genes and expression profiles even in model plants. In contrast, wild plants inhabiting coastal environments have acquired salt tolerance, often by enhancing the mechanisms that are also conserved in model plants. Elucidating the mechanisms and underlying genes in such wild plants should provide a clear guidance to the combinations of appropriate genes. The genus Vigna represents such wild plants because of its great diversity. Recent studies have revealed that multiple Vigna species have independently evolved salt tolerance in various ways. Some of the species are studied in detail, highlighting the significance of combining and pyramiding multiple mechanisms for improving salt tolerance of a plant.

‘MK5601’ is an improved tea cultivar with genetic material from Camellia taliensis, a wild relative of the tea plant, Camellia sinensis. ‘MK5601’ differs from common tea cultivars in being rich in hydrolyzable tannins such as theogallin and G-strictinin, which have presumed health benefits. We identified two quantitative trait locus (QTL) clusters with powerful effects on hydrolyzable tannin contents in a population derived from a cross between ‘MK5601’ and an elite green tea cultivar ‘Saeakari’. The C. taliensis-type alleles at each locus in ‘MK5601’ increased the hydrolyzable tannin contents. The two QTL clusters were detected in 2 years and were confirmed in another population. These clusters have pleiotropic effects on tannin biosynthesis, as they are associated also with catechin contents. There was a strong negative correlation between the contents of hydrolyzable tannins and non-galloylated catechins. Despite the remarkable compositional changes, the two QTL clusters did not affect tea flavor. These QTLs provide important basic knowledge for developing new tea cultivars and tea products with high contents of hydrolyzable tannins and good health-promoting effects.

The process by which day length affects rice heading has been studied on a molecular basis; however, little is known about the traits that occur with heading, such as heading synchrony, premature heading, and day of the determined effective tiller number. These traits vary more in photo-insensitive (photo-In) lines than in day-length-sensitive lines. We used photo-in lines to study the associations of these traits with heading earliness and the influence of the earliness genes and the different latitudes. The results of this study showed these traits were significantly correlated with the earliness of first days to heading (F-DTH) among the photo-In lines. A wider range of F-DTH was observed in Sapporo than Iga when used the same photo-In varieties, which was confirmed under artificial conditions. We identified five significant quantitative trait loci (QTL) for F-DTH among the photo-In lines. A QTL with a major effect associated with F-DTH, heading synchrony, and premature heading was detected on chromosome 4. Using photo-In lines, we propose a heat-tolerance strategy for early cultivation in low-latitude regions.

The radiocesium contamination of food poses a serious threat to food safety because radiocesium has a long half-life and emits harmful radiation during decay. Therefore, it is important to reduce radiocesium uptake by crops. In this study, we identified low-cesium-accumulating soybean mutants from an ethyl methanesulfonate-induced mutant population. Through the phenotypic screening of the population based on the seed cesium concentration, 10 candidate low-cesium-accumulating mutant lines were selected. Five of these exhibited significantly reduced seed radiocesium concentrations compared with the original variety, and one had accumulated an excessive amount of sodium. Since plant intracellular sodium ion homeostasis is regulated by the salt overly sensitive (SOS) pathway, sequence analysis of GmSOS1, which encodes an Na⁺/H⁺ antiporter in this pathway, revealed that the high-sodium-accumulating line contains a mutation in this gene. Additionally, two more gmsos1 mutant lines were isolated from the mutant population. In the field trial, the three independent gmsos1 mutant lines possessed lower seed cesium concentrations than the wild type. These results indicate that GmSOS1 is responsible for seed cesium accumulation, and gmsos1 mutants are potential breeding materials for reducing hazardous radiocesium accumulation in soybeans.

Iron toxicity, caused by excessive iron uptake, can reduce biomass and yield in rice (Oryza sativa L.). In this report, we present a wide genetic variation among 91 varieties, including 18 upland NERICAs, in terms of leaf bronzing score (LBS), dry weight under iron toxicity (Iron-DW), dry weight under control conditions (Control-DW), and relative dry weight (RDW = Iron-DW/Control-DW), using agar nutrient solution at rice seedling stage. We found no correlations between LBS and the other three. These were classified into three clusters: A, B1 and B2, based on these trait variations. Cluster A consists mainly of lowland Japonica and Indica Groups, exhibiting the lowest LBS and RDW that were intermediate between B1 and B2. Clusters B1 and B2 included both Japonica and Indica Groups’ varieties, as well as the 18 upland NERICAs. B1 displayed the highest RDW and a LBS that was intermediate between A and B2. Conversely, B2 had the highest LBS and the lowest RDW. Both the Indica and Japonica Groups displayed extensive variation in tolerance to iron toxicity. Moreover, LBS and RDW are controlled by different genetic mechanisms. In our association analysis using NERICAs, we identified two quantitative trait loci (QTLs): one for LBS on chromosome 9, which is a novel discovery, and another for Control-DW, which enhances tolerance through O. glaberrima alleles.

Pungency levels (capsaicinoid content) are critical traits influencing the quality and commercial value of chili peppers (Capsicum annuum). However, their complex inheritance patterns make controlling them challenging when crossing different progeny in current breeding programs. As a potential solution, we explored genomic prediction (GP) for crossing different progeny based solely on parental data. In this initial study, we assessed the feasibility of GP in 156 F₁ accessions derived from 20 parents within 132 inbred C. annuum accessions. Capsaicinoid content (capsaicin, dihydrocapsaicin, and their total) was quantified using high-performance liquid chromatography. Inheritance analysis revealed that nearly half of the F₁ accessions exhibited high-parent heterosis (F₁ > higher parent), particularly in crosses between lower-pungency parents. We then performed GP for F₁ accessions using 3,149 single nucleotide polymorphisms from inbred accessions. Among 11 models tested, GBLUP-GAUSS tended to show high accuracy, with predicted values showing a significant positive correlation (r = 0.770, P < 0.01) with observed capsaicinoid content (μg·gDW^–1), although the involvement of heterosis in reducing accuracy was observed. These findings suggest that GP can effectively rank pungency levels among F₁ progeny based solely on parental information, providing valuable insights for developing GP-based breeding strategies in chili pepper.

Despite the development of several cultural pest controls, foot rot disease has severely damaged sweetpotato crops in southern Japan since 2018. A more effective solution would be to breed resistant cultivars. To promote the breeding of cultivars whose stems are resistant to this disease, we previously developed a laboratory resistance test using sweetpotato stems. The laboratory test can indirectly evaluate the foot rot resistance of stems in the field test, which is usually used to evaluate cultivar resistance in breeding programs. In the present study, we improved laboratory test by using sweetpotato storage roots and investigated the resistance of storage roots of 46 cultivars. We analyzed the correlations of various indices of resistance of storage roots between the laboratory test and the field test, and found that the index of the laboratory storage root test correlated significantly with the proportion of severely rotted storage roots in the field test in some cases. This result indicated that the laboratory storage roots test could indirectly evaluate the foot rot resistance of storage roots in the field test. These two laboratory tests using stems and storage roots could help breed cultivars whose stems and storage roots are resistant to foot rot.

Rice brown spot (BS), caused by Bipolaris oryzae, is the third most prevalent rice disease in Japan and causes yield losses. In this study, quantitative trait loci (QTLs) associated with BS resistance were identified from the indica cultivars ‘Tupa 121-3’, ‘Naba’, and ‘IR58’. Two QTLs, qBSR6-kt (from ‘Tupa 121-3’) and qBSR11-kn (from ‘Naba’), were detected through QTL analysis of two F₂ populations derived from crosses between the BS-susceptible japonica cultivar ‘Koshihikari’ and two resistant lines selected from chromosome segment substitution lines with chromosome segments from ‘Tupa 121-3’ and ‘Naba’ in the ‘Koshihikari’ genetic background. Another three QTLs from ‘IR58’ (qBSR2-im, qBSR11-im, and qBSR12-im) were detected by QTL analysis of recombinant inbred lines derived from a cross between ‘IR58’ and the BS-susceptible japonica cultivar ‘Mienoyume’. Among these detected QTLs, qBSR6-kt, qBSR11-kn, and qBSR11-im were confirmed to confer effective BS resistance in japonica rice cultivars. The two QTLs qBSR11-kn and qBSR11-im were located near the previously reported BS resistance QTL bsr1 on chromosome 11. BS resistance QTL qBSR6-kt (on chromosome 6) was identified as a novel QTL that confers effective resistance to BS and may be valuable for pyramiding with bsr1 or other BS resistance QTLs.

In many yellow soybean (Glycine max) cultivars grown in Japan, pigmentation is suppressed throughout the seed coat, including the hilum region. This phenomenon is due to naturally occurring RNA silencing of chalcone synthase (CHS) genes, which is induced by the I allele of the I locus. A candidate for the I allele, designated GmIRCHS, includes inverted repeats of the pseudoCHS gene and is clustered with the ICHS1 gene. Fully pigmented seeds are sometimes produced by yellow soybean cultivars as a result of a spontaneous mutation. The causal DNA changes are deletions that involve GmIRCHS. While small deletions of 0.8–3.3 kb have been previously characterized, the details for larger deletions remain unknown. Here, we characterized these large deletions using a recently released whole-genome sequence for the Japanese yellow soybean cultivar ‘Enrei’. The deletions encompass 17- to 38-kb DNA regions, which involve GmIRCHS and some or all of the neighboring genes GmJ1, P450, Transferase, and ICHS1. These data suggest that the DNA region surrounding GmIRCHS is prone to large structural changes, leading to reversion to pigmentation of the seed coat.