RNA silencing as a tool to uncover gene function and engineer novel traits in soybean

RNA silencing refers collectively to diverse RNA-mediated pathways of nucleotide-sequence-specific inhibition of gene expression. It has been used to analyze gene function and engineer novel traits in various organisms. Here, we review the application of RNA silencing in soybean. To produce soybean lines, in which a particular gene is stably silenced, researchers have frequently used a transgene that transcribes inverted repeats of a target gene segment. Suppression of gene expression in developing soybean embryos has been one of the main focuses of metabolic engineering using transgene-induced silencing. Plants that have enhanced resistance against diseases caused by viruses or cyst nematode have also been produced. Meanwhile, Agrobacterium rhizogenes-mediated transformation has been used to induce RNA silencing in roots, which enabled analysis of the roles of gene products in nodulation or disease resistance. RNA silencing has also been induced using viral vectors, which is particularly useful for gene function analysis. So far, three viral vectors for virus-induced gene silencing have been developed for soybean. One of the features of the soybean genome is the presence of a large number of duplicated genes. Potential use of RNA silencing technology in combination with forward genetic approaches for analyzing duplicated genes is discussed.     

Genetics of seed coat colour in lentil

Summary Four grey mottled seed coat colour lentil lines/cultivars were crossed to one brown seed coat colour cultivar. The F₁ hybrids were brown seeded in all the crosses. Segregation pattern for seed coat colour in F₂ and F₃ generations revealed that it is under control of a single dominant gene, which is present in the parent UPL 175 while a recessive gene is responsible for grey mottled seed coat colour in Pant L 406, Pant L 639, LG 120 and Rau 101.     

Wide genetic variation in phenolic compound content of seed coats among black soybean cultivars

Black soybeans have been used as a food source and also in traditional medicine because their seed coats contain natural phenolic compounds such as proanthocyanidin and anthocyanin. The objective of this research is to reveal the genetic variation in the phenolic compound contents (PCCs) of seed coats in 227 black soybean cultivars, most of which were Japanese landraces and cultivars. Total phenolics were extracted from seed coats using an acidic acetone reagent and the proanthocyanidin content, monomeric anthocyanin content, total flavonoids content, total phenolics content, and radical scavenging activity were measured. The cultivars showed wide genetic variation in PCCs. Each of the contents was highly correlated with one another, and was closely associated with radical scavenging activity. PCCs were also moderately associated by flowering date but not associated by seed weight. Cultivars with purple flowers had a tendency to produce higher PCCs compared with cultivars with white flowers, suggesting that the W1 locus for flower color can affect phenolic compound composition and content. Our results suggest that developing black soybean cultivars with high functional phenolic compounds activity is feasible.     

Genetic analysis of net-like cracking in soybean seed coats

Cracking of seed coats in soybean (Glycine max (L.) Merr.) deteriorates the external appearance of seeds and reduces their commercial value. Two types of cracking have been reported that occur in some cultivars: Type I with irregular cracks and Type II with net-like cracks. This study was conducted to determine the genetic basis of net-like cracking. Genetic analysis was performed using F₁ plants produced by crossing Uzuramame, a Japanese landrace with black seed coats having net-like cracking and a Clark mutant with black seed coats, their F₂ population and F₃ lines. Degree of cracking in individual plants was calculated by averaging cracking index (no cracking: 0 to severe cracking: 4) of total or 100-seed samples (average cracking index, ACI). Uzuramame exhibited intense cracking, whereas the Clark mutant showed slight cracking. Intermediate degree of cracking in F₁ plants suggested incomplete dominance. ACI of F₂ plants was continuously distributed. Gene number involved was estimated to be 1.4 by Wright's method. All F₃ lines derived from F₂ plants with ACI more than 2.8 displayed severe cracking phenotypes. In contrast, F₃ lines derived from F₂ plants with ACI less than 2.8 segregated from low to high ACI (0.5 to 3.2). When F₂ plants were classified as slight (ACI<2.8) or severe (ACI>2.8) cracking, the frequency distribution of the F₂ plants fitted to a 3:1 ratio. Genotypes of SSR marker Satt264 that is closely linked to SoyPRP1 locus for proline-rich cell wall protein had a minor effect on ACI. Further, seed weight was positively associated with ACI (r =0.46^**). Our results suggest that net-like cracking is controlled primarily by a major gene, and SoyPRP1 and gene(s) contributing to seed weight may have minor effects on the intensity of cracking. This revised version was published online in July 2006 with corrections to the Cover Date.     

A pubescence color gene enhances tolerance to cold-induced seed cracking in yellow soybean

In yellow soybean, severe cold weather causes seed cracking on the dorsal side. Yellow soybeans carry the I or iⁱ allele of the I locus and have a yellow (I) or pigmented (iⁱ) hilum. We previously isolated an additional allele, designated as Ic, of the I locus, and reported that yellow soybeans with the IcIc genotype may be tolerant to cold-induced seed cracking. The Ic allele by itself, however, does not confer high tolerance. The association of a pubescence color gene (T) with suppression of low-temperature-induced seed coat deterioration has been previously reported. In the present study, we tested whether T is effective for the suppression of cold-induced seed cracking using two pairs of near-isogenic lines for the T locus in the iⁱiⁱ or IcIc background. In both backgrounds, the cracked seed rate of the near-isogenic line with the TT genotype was significantly lower than that with the tt genotype, which indicates that T has an inhibitory effect on cold-induced seed cracking. Furthermore, we also showed that gene pyramiding of Ic and T can improve tolerance to cold-induced seed cracking. Our findings should aid the development of highly SC-tolerant cultivars in soybean breeding programs.     

Development of IP and SCAR markers linked to the yellow seed color gene in Brassica juncea L.

Previous studies showed that the yellow seed color gene of a yellow mustard was located on the A09 chromosome. In this study, the sequences of the molecular markers linked to the yellow seed color gene were analyzed, the gene was primarily mapped to an interval of 23.304 to 29.402M. Twenty genes and eight markers’ sequences in this region were selected to design the IP and SCAR primers. These primers were used to screen a BC₈S₁ population consisting of 1256 individuals. As a result, five IP and five SCAR markers were successfully developed. IP4 and Y1 were located on either side of the yellow seed color gene at a distance of 0.1 and 0.3 cM, respectively. IP1, IP2 and IP3 derived from Bra036827, Bra036828, Bra036829 separately, co-segregated with the target gene. BLAST analysis indicated that the sequences of newly developed markers showed good collinearity with those of the A09 chromosome, and that the target gene might exist between 27.079 and 27.616M. In light of annotations of the genes in this region, only Bra036828 is associated with flavonoid biosynthesis. This gene has high similarity with the TRANSPARENT TESTA6 gene, Bra036828 was hence identified as being the gene possibly responsible for yellow seed color, in our research.     

The genetics of hard seed coat in the genus Lens

Summary Seeds of the cultivated lentil are capable of germinating shortly after maturation. The seed dormancy of wild lentil species is due to a hard seed coat. In crosses between the cultivated species L. culinaris and its wild progenitor L. orientalis the hard seed coat of the wild species was controlled by a single recessive gene in homozygous condition. In a cross between the wild species L. ervoides and L. culinaris the hard seed coat of L. ervoides was controlled by a single dominant gene. The significance of the genetics of seed coat hardness in the domestication of lentil is briefly discussed.     

Diversity of seed cesium accumulation in soybean mini-core collections

Radiocesium is an extremely harmful radionuclide because of its long half-life; it is important to reduce its transfer from contaminated soil into crops. Here we surveyed genetic variation for seed cesium (Cs) concentration in soybean mini-core collections representing large genetic diversity. The collections grown over 3 years in rotational paddy fields exhibited varying seed Cs concentrations with significant year-to-year correlations, although the phenotypic stability of Cs concentration was lower than that of the congeners potassium (K) and rubidium (Rb). Although Cs is supposedly accumulated in plants via the K transport system, there was no apparent relationship between Cs and K concentrations, whereas a clear positive correlation was observed between Cs and Rb concentrations. Cs and K concentrations in seed showed slightly positive and negative correlations, respectively, with days to flowering. We selected several high or low Cs accumulator candidates on the basis of the 3 years of seed concentration data. These two groups showed significantly different seed Cs concentrations in another field. The differences could not be explained by flowering time alone. These results suggest that genetic variation for seed Cs concentration is present in soybean germplasm and would be useful for breeding low Cs-accumulating varieties.     

Genetic relationships of soybean cyst nematode resistance originated in Gedenshirazu and PI84751 on Rhg1 and Rhg4 loci

Soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) is one of the most damaging pests of soybean (Glycine max (L.) Merr.). Host plant resistance has been the most effective control method. Because of the spread of multiple SCN races in Hokkaido, the Tokachi Agricultural Experiment Station has bred soybeans for SCN resistance since 1953 by using 2 main resistance resources PI84751 (resistant to races 1 and 3) and Gedenshirazu (resistant to race 3). In this study, we investigated the genetic relationships of SCN resistance originating from major SCN resistance genes in Gedenshirazu and PI84751 by using SSR markers. We confirmed that race 1 resistance in PI84751 was independently controlled by 4 genes, 2 of which were rhg1 and Rhg4. We classified the PI84751- type allele of Rhg1 as rhg1-s and the Gedenshirazu-type allele of Rhg1 as rhg1-g. In the cross of the Gedenshirazu-derived race 3-resistant lines and the PI84751-derived races 1- and 3-resistant lines, the presence of rhg1-s and Rhg4 was responsible for race 1-resistance. These results indicated that it was possible to select race 1 resistant plants by using marker-assisted selection for the rhg1-s and Rhg4 alleles through a PI84751 origin × Gedenshirazu origin cross.     

Inheritance of seed coat colour in broad bean (Vicia faba L.)

Summary The inheritance of the seed coat colours violet, spotted, brown, green, red, black and beige was investigated in a 10×10 diallel cross between broad bean (Vicia faba L. major) lines. Spotted seed colour was dominant over any uniform seed coat colouring. Brown was dominant over black, green and normal (beige colour). Black and red seed parents behaved as recessive in all F₁ progenies. A 3 (coloured): 1 (normal) segregation ratio was observed in the F₂ of crosses of violet, brown, black, red and spotted seed coat parents to nornal seed coloured parents. Green x beige gave a segregation ratio of 9:7 in F₂. When two parents with different seed coat colour were involved in a cross, the F₂ showed a typical digenic segregation ratio thus demonstrating two unlinked and sometimes epistatic loci.Segregation of a multiallelic series at two loci explains all segregation ratios observed for seed coat colour in broad bean.     

Combining ability of seed vigor and seed yield in soybean

Studies have shown no consensus in relationships between seed yield and vigor in soybean [Glycine max (L.) Merrill]. The lack of information regarding the inheritance of seed vigor prompted this study to determine the types of gene action and combining ability estimates for seed vigor and its related traits. Five high and six low seed vigor soybean genotypes were crossed in a diallel, and selfed to produce 55 F₂ progenies, which were examined, along with the parents, for seed vigor, yield, and seed weight. Significant genotype and environment effects were found for seed vigor and yield. General combining ability (GCA) effects for seed vigor and seed yield were significant (p≤ 0.01) and larger than specific combining ability (SCA) effects. Significant GCA and SCA effects were found for seed weight, indicating that both additive and non additive genetic effects were involved in conditioning seed weight. The ratios of mean square, 2GCA / (2GCA+SCA), were 0.96 for seed vigor and 0.93 for seed yield. These ratios indicated that additive gene effects were more important than non additive gene effects for seed vigor and seed yield in these crosses. Mean seed vigor(83.8%), as determined by accelerated aging germination, and mean seed yield (2,155 kg ha^-1)in high vigor × high vigor crosses were higher than the high vigor × low vigor and low vigor × low vigor crosses. Mean percent accelerated aging germination rates in F₂ populations from diallel crosses were significantly related to mid-parent seed vigor(r² = 0.52^**) and midparent seed size (r² = 0.31^**). These results indicated that levels of seed vigor can be improved through breeding, while maintaining high yields because of the predominance of GCA effects in both seed vigor and seed yield. This revised version was published online in July 2006 with corrections to the Cover Date.     

Fine mapping of foxglove aphid (Aulacorthum solani) resistance gene Raso1 in soybean and its effect on tolerance to Soybean dwarf virus transmitted by foxglove aphid

Soybean dwarf virus (SbDV) causes serious dwarfing, yellowing and sterility in soybean (Glycine max). The soybean cv. Adams is tolerant to SbDV infection in the field and exhibits antibiosis to foxglove aphid (Aulacorthum solani), which transmits SbDV. This antibiosis (termed “aphid resistance”) is required for tolerance to SbDV in the field in segregated progenies of Adams. A major quantitative trait locus, Raso1, is reported for foxglove aphid resistance. Our objectives were to fine map Raso1 and to reveal whether Raso1 alone is sufficient to confer both aphid resistance and SbDV tolerance. We introduced Raso1 into cv. Toyomusume by backcrossing and investigated the degree of aphid antibiosis to foxglove aphid and the degree of tolerance to SbDV in the field. All Raso1-introduced backcross lines showed aphid resistance. Interestingly, only one Raso1-introduced backcross line (TM-1386) showed tolerance to SbDV in the field. The results demonstrated Raso1 alone is sufficient to confer aphid resistance but insufficient for SbDV tolerance. Tolerance to SbDV was indicated to require additional gene(s) to Raso1. Additionally, Raso1 was mapped to a 63-kb interval on chromosome 3 of the Williams 82 sequence assembly (Glyma1). This interval includes a nucleotide-binding site–leucine-rich repeat encoding gene and two other genes in the Williams 82 soybean genome sequence.     

Transfer of the Rsv3 locus from ‘Harosoy’ for resistance to soybean mosaic virus strains C and D in Japan

Resistance to soybean mosaic virus (SMV) is imperative for soybean (Glycine max (L.) Merr.) production in the Tohoku region. Molecular markers for SMV resistance were previously reported for U.S. SMV strains, but they cannot be applied because of the differences in strain classification between Japan and the U.S. A U.S. variety ‘Harosoy’ has been used mainly as a donor of resistance to SMV strains C and D in a Japanese breeding program, resulting in resistant varieties such as ‘Fukuibuki.’ Because ‘Harosoy’ harbors the Rsv3 gene conferring resistance to the virulent SMV strain groups, G5 through G7, it appears that the Rsv3 gene confers resistance to strains C and D. In this study, we introduced resistance to the two strains from ‘Fukuibuki’ into a leading variety ‘Ohsuzu’ by recurrent backcrossing with marker-assisted selection. All lines selected with markers near Rsv3 showed resistance to the strains, suggesting that the Rsv3 locus is responsible for the resistance. Three years of trials showed that one of the breeding lines, ‘Tohoku 169,’ was equivalent to ‘Ohsuzu’ with respect to agricultural characteristics such as seed size, maturity date, and seed yield, except for the SMV resistance.     

Evolutionary and comparative analyses of the soybean genome

The soybean genome assembly has been available since the end of 2008. Significant features of the genome include large, gene-poor, repeat-dense pericentromeric regions, spanning roughly 57% of the genome sequence; a relatively large genome size of ~1.15 billion bases; remnants of a genome duplication that occurred ~13 million years ago (Mya); and fainter remnants of older polyploidies that occurred ~58 Mya and >130 Mya. The genome sequence has been used to identify the genetic basis for numerous traits, including disease resistance, nutritional characteristics, and developmental features. The genome sequence has provided a scaffold for placement of many genomic feature elements, both from within soybean and from related species. These may be accessed at several websites, including http://www.phytozome.net, http://soybase.org, http://comparative-legumes.org, and http://www.legumebase.brc.miyazaki-u.ac.jp. The taxonomic position of soybean in the Phaseoleae tribe of the legumes means that there are approximately two dozen other beans and relatives that have undergone independent domestication, and which may have traits that will be useful for transfer to soybean. Methods of translating information between species in the Phaseoleae range from design of markers for marker assisted selection, to transformation with Agrobacterium or with other experimental transformation methods.     

Genetic analysis of variations in the sugar chain composition at the C-3 position of soybean seed saponins

Saponins are sterols or triterpene glycosides that are widely distributed in plants. The biosynthesis of soybean saponins is thought to involve many kinds of glycosyltransferases, which is reflected in their structural diversity. Here, we performed linkage analyses of the Sg-3 and Sg-4 loci, which may control the sugar chain composition at the C-3 sugar moieties of the soybean saponin aglycones soyasapogenols A and B. The Sg-3 locus, which controls the production of group A saponin Af, was mapped to chromosome (Chr-) 10. The Sg-4 locus, which controls the production of DDMP saponin βa, was mapped to Chr-1. To elucidate the preference of sugar chain formation at the C-3 and C-22 positions, we analyzed the F₂ population derived from a cross between a mutant variety, Kinusayaka (sg-1⁰), for the sugar chain structure at C-22 position, and Mikuriya-ao (sg-3), with respect to the segregation of the composition of the group A saponins, and found that the formation of these sugar chains was independently regulated. Furthermore, a novel saponin, predicted to be A0-γg, 3-O-[β-d-galactopyranosyl (1→2)-β-d-glucuronopyranosyl]-22-O-α-l-arabinopyranosyl-soyasapogenol A, appeared in the hypocotyl of F₂ individuals with genotype sg-1⁰/sg-1⁰ sg-3/sg-3.     

Effects on flowering and seed yield of dominant alleles at maturity loci E2 and E3 in a Japanese cultivar,Enrei

‘Enrei’ is the second leading variety of soybean (Glycine max (L.) Merr.) in Japan. Its cultivation area is mainly restricted to the Hokuriku region. In order to expand the adaptability of ‘Enrei’, we developed two near-isogenic lines (NILs) of ‘Enrei’ for the dominant alleles controlling late flowering at the maturity loci, E2 and E3, by backcrossing with marker-assisted selection. The resultant NILs and the original variety were evaluated for flowering, maturity, seed productivity and other agronomic traits in five different locations. Expectedly, NILs with E2 or E3 alleles flowered later than the original variety in most locations. These NILs produced comparatively larger plants in all locations. Seed yields were improved by E2 and E3 in the southern location or in late-sowing conditions, whereas the NIL for E2 exhibited almost the same or lower productivity in the northern locations due to higher degrees of lodging. Seed quality-related traits, such as 100-seed weight and protein content, were not significantly different between the original variety and its NILs. These results suggest that the modification of genotypes at maturity loci provides new varieties that are adaptive to environments of different latitudes while retaining almost the same seed quality as that of the original.     

Rj (rj) genes involved in nitrogen-fixing root nodule formation in soybean

It has long been known that formation of symbiotic root nodules in soybean (Glycine max (L.) Merr.) is controlled by several host genes referred to as Rj (rj) genes, but molecular cloning of these genes has been hampered by soybean’s complicated genome structure and large genome size. Progress in molecular identification of legume genes involved in root nodule symbiosis have been mostly achieved by using two model legumes, Lotus japonicus and Medicago truncatula, that have relatively simple and small genomes and are capable of molecular transfection. However, recent development of resources for soybean molecular genetic research, such as genome sequencing, large EST databases, and high-density linkage maps, have enabled us to isolate several Rj genes. This progress has been achieved in connection with systematic utilization of the information obtained from molecular genetics of the model legumes. In this review, we summarize the current status of knowledge of host-controlled nodulation in soybean based on information from recent studies on Rj genes, and discuss the future research prospects.     

Effect of quantitative trait loci for seed shattering on abscission layer formation in Asian wild rice Oryza rufipogon

Asian cultivated rice Oryza sativa L. was domesticated from its wild ancestor, O. rufipogon. During domestication, the cultivated rice lost its seed-shattering behaviour. Previous studies have shown that two major quantitative trait loci (QTLs; qSH1 and sh4) are responsible for the seed-shattering degree. Here, we produced introgression lines carrying non-functional alleles from O. sativa ‘Nipponbare’ at the two major QTLs in the genetic background of wild rice O. rufipogon W630, and examined the effects of the two QTLs on seed shattering and abscission layer formation. The introgression lines, with Nipponbare alleles at either or both loci, showed complete or partial abscission layer formation, respectively, indicating that other unknown loci might be involved in enhancing seed shattering in wild rice. We detected a single QTL named qSH3 regulating seed-shattering degree using an F₂ population between Nipponbare and the introgression line carrying Nipponbare alleles at the two QTLs. Although we generated an introgression line for qSH3 alone, no effects on seed shattering were observed. However, a significant effect on seed-shattering degree was observed for the introgression line carrying Nipponbare alleles at qSH3 and the two QTLs, suggesting an important role of qSH3 on seed shattering in coordination with the two QTLs.