Distribution of photoperiod-insensitive alleles Ppd-B1a and Ppd-D1a and their effect on heading time in Japanese wheat cultivars

The genotypes of photoperiod response genes Ppd-B1 and Ppd-D1 in Japanese wheat cultivars were determined by a PCR-based method, and heading times were compared among genotypes. Most of the Japanese wheat cultivars, except those from the Hokkaido region, carried the photoperiod-insensitive allele Ppd-D1a, and heading was accelerated 10.3 days compared with the Ppd-D1b genotype. Early cultivars with Ppd-D1a may have been selected to avoid damage from preharvest rain. In the Hokkaido region, Ppd-D1a frequency was lower and heading date was late regardless of Ppd-D1 genotype, suggesting another genetic mechanism for late heading in Hokkaido cultivars. In this study, only 11 cultivars proved to carry Ppd-B1a, and all of them carried another photoperiod-insensitive allele, Ppd-D1a. The Ppd-B1a/Ppd-D1a genotype headed 6.7 days earlier than the Ppd-B1b/Ppd-D1a genotype, indicating a significant effect of Ppd-B1a in the genetic background with Ppd-D1a. Early-maturity breeding in Japan is believed to be accelerated by the introduction of the Ppd-B1a allele into medium-heading cultivars carrying Ppd-D1a. Pedigree analysis showed that Ppd-B1a in three extra-early commercial cultivars was inherited from ‘Shiroboro 21’ by early-heading Chugoku lines bred at the Chugoku Agriculture Experimental Station.     

Differential contribution of two Ppd-1 homoeoalleles to early-flowering phenotype in Nepalese and Japanese varieties of common wheat

Wheat landraces carry abundant genetic variation in heading and flowering times. Here, we studied flowering-related traits of two Nepalese varieties, KU-4770 and KU-180 and a Japanese wheat cultivar, Shiroganekomugi (SGK). These three wheat varieties showed similar flowering time in a common garden experiment. In total, five significant quantitative trait loci (QTLs) for three examined traits, the heading, flowering and maturation times, were detected using an F₂ population of SGK/KU-4770. The QTLs were found at the Ppd-1 loci on chromosomes 2B and 2D and the 2B QTL was also confirmed in another F₂ population of SGK/KU-180. The Ppd-D1 allele from SGK and the Ppd-B1 alleles from the two Nepalese varieties might be causal for early-flowering phenotype. The SGK Ppd-D1 allele contained a 2-kb deletion in the 5′ upstream region, indicating a photoperiod-insensitive Ppd-D1a allele. Real-time PCR analysis estimating the Ppd-B1 copy number revealed that the two Nepalese varieties included two intact Ppd-B1 copies, putatively resulting in photoperiod insensitivity and an early-flowering phenotype. The two photoperiod-insensitive Ppd-1 homoeoalleles could independently contribute to segregation of early-flowering individuals in the two F₂ populations. Therefore, wheat landraces are genetic resources for discovery of alleles useful for improving wheat heading or flowering times.     

Distribution of the photoperiod insensitive <Emphasis Type="Italic">Ppd-D1a</Emphasis> allele in Chinese wheat cultivars

Photoperiod response is of great importance for optimal adaptation of bread wheat cultivars to specific environments, and variation is commonly associated with allelic differences at the Ppd-D1 locus on chromosome 2D. A total of 926 Chinese wheat landraces and improved cultivars collected from nine wheat growing zones were tested for their genotypes at the Ppd-D1 locus using allele-specific markers. The average frequency of the photoperiod-insensitive Ppd-D1a allele was 66.0%, with the frequencies of 38.6 and 90.6% in landraces and improved cultivars, respectively. However, the Ppd-D1a allele was present in all improved cultivars released after 1970 except for spring wheats in high latitude northwestern China, and winter wheats in Gansu and Xinjiang. The presence of the Ppd-D1a allele in landraces and improved cultivars increased gradually from north to south, illustrating the relationship between photoperiod response and environment. Ppd-D1a in Chinese wheats is derived from three sources, Japanese landrace Akagomughi and Chinese landraces Mazhamai and Youzimai. The current information is important for understanding the broad adaptation of improved Chinese wheat cultivars. F. P. Yang and X. K. Zhang contributed equally to this work.     

Evaluation of the effects of five QTL regions on Fusarium head blight resistance and agronomic traits in spring wheat (Triticum aestivum L.)

Fusarium head blight (FHB) is an important disease of wheat (Triticum aestivum L.). The aim of this study was to determine the effects of quantitative trait locus (QTL) regions for resistance to FHB and estimate their effects on reducing FHB damage to wheat in Hokkaido, northern Japan. We examined 233 F₁-derived doubled-haploid (DH) lines from a cross between ‘Kukeiharu 14’ and ‘Sumai 3’ to determine their reaction to FHB during two seasons under field conditions. The DH lines were genotyped at five known FHB-resistance QTL regions (on chromosomes 3BS, 5AS, 6BS, 2DL and 4BS) by using SSR markers. ‘Sumai 3’ alleles at the QTLs at 3BS and 5AS effectively reduced FHB damage in the environment of Hokkaido, indicating that these QTLs will be useful for breeding spring wheat cultivars suitable for Hokkaido. Some of the QTL regions influenced agronomic traits: ‘Sumai 3’ alleles at the 4BS and 5AS QTLs significantly increased stem length and spike length, that at the 2DL QTL significantly decreased grain weight, and that at the 6BS QTL significantly delayed heading, indicating pleiotropic or linkage effects between these agronomic traits and FHB resistance.     

Identification of QTLs for fruit quality traits in Japanese apples: QTLs for early ripening are tightly related to preharvest fruit drop

Many important apple (Malus × domestica Borkh.) fruit quality traits are regulated by multiple genes, and more information about quantitative trait loci (QTLs) for these traits is required for marker-assisted selection. In this study, we constructed genetic linkage maps of the Japanese apple cultivars ‘Orin’ and ‘Akane’ using F₁ seedlings derived from a cross between these cultivars. The ‘Orin’ map consisted of 251 loci covering 17 linkage groups (LGs; total length 1095.3 cM), and the ‘Akane’ map consisted of 291 loci covering 18 LGs (total length 1098.2 cM). We performed QTL analysis for 16 important traits, and found that four QTLs related to harvest time explained about 70% of genetic variation, and these will be useful for marker-assisted selection. The QTL for early harvest time in LG15 was located very close to the QTL for preharvest fruit drop. The QTL for skin color depth was located around the position of MYB1 in LG9, which suggested that alleles harbored by ‘Akane’ are regulating red color depth with different degrees of effect. We also analyzed soluble solids and sugar component contents, and found that a QTL for soluble solids content in LG16 could be explained by the amount of sorbitol and fructose.     

Close linkage of a blast resistance gene,Pias(t), with a bacterial leaf blight resistance gene,Xa1-as(t), in a rice cultivar ‘Asominori’

It has long been known that a bacterial leaf blight-resistant line in rice obtained from a crossing using ‘Asominori’ as a resistant parent also has resistance to blast, but a blast resistance gene in ‘Asominori’ has not been investigated in detail. In the present study, a blast resistance gene in ‘Asominori’, tentatively named Pias(t), was revealed to be located within 162-kb region between DNA markers YX4-3 and NX4-1 on chromosome 4 and to be linked with an ‘Asominori’ allele of the bacterial leaf blight resistance gene Xa1, tentatively named Xa1-as(t). An ‘Asominori’ allele of Pias(t) was found to be dominant and difference of disease severity between lines having the ‘Asominori’ allele of Pias(t) and those without it was 1.2 in disease index from 0 to 10. Pias(t) was also closely linked with the Ph gene controlling phenol reaction, suggesting the possibility of successful selection of blast resistance using the phenol reaction. Since blast-resistant commercial cultivars have been developed using ‘Asominori’ as a parent, Pias(t) is considered to be a useful gene in rice breeding for blast resistance.     

Confirming a major QTL and finding additional loci responsible for field resistance to brown spot (Bipolaris oryzae) in rice

Brown spot is a devastating rice disease. Quantitative resistance has been observed in local varieties (e.g., ‘Tadukan’), but no economically useful resistant variety has been bred. Using quantitative trait locus (QTL) analysis of recombinant inbred lines (RILs) from ‘Tadukan’ (resistant) × ‘Hinohikari’ (susceptible), we previously found three QTLs (qBS2, qBS9, and qBS11) that conferred resistance in seedlings in a greenhouse. To confirm their effect, the parents and later generations of RILs were transplanted into paddy fields where brown spot severely occurred. Three new resistance QTLs (qBSfR1, qBSfR4, and qBSfR11) were detected on chromosomes 1, 4, and 11, respectively. The ‘Tadukan’ alleles at qBSfR1 and qBSfR11 and the ‘Hinohikari’ allele at qBSfR4 increased resistance. The major QTL qBSfR11 coincided with qBS11 from the previous study, whereas qBSfR1 and qBSfR4 were new but neither qBS2 nor qBS9 were detected. To verify the qBSfR1 and qBSfR11 ‘Tadukan’ resistance alleles, near-isogenic lines (NILs) with one or both QTLs in a susceptible background (‘Koshihikari’) were evaluated under field conditions. NILs with qBSfR11 acquired significant field resistance; those with qBSfR1 did not. This confirms the effectiveness of qBSfR11. Genetic markers flanking qBSfR11 will be powerful tools for marker-assisted selection to improve brown spot resistance.     

Molecular and genealogical analysis of grain dormancy in Japanese wheat varieties,with specific focus on MOTHER OF FT AND TFL1 on chromosome 3A

In the wheat (Triticum aestivum L.) cultivar ‘Zenkoujikomugi’, a single nucleotide polymorphism (SNP) in the promoter of MOTHER OF FT AND TFL1 on chromosome 3A (MFT-3A) causes an increase in the level of gene expression, resulting in strong grain dormancy. We used a DNA marker to detect the ‘Zenkoujikomugi’-type (Zen-type) SNP and examined the genotype of MFT-3A in Japanese wheat varieties, and we found that 169 of 324 varieties carry the Zen-type SNP. In Japanese commercial varieties, the frequency of the Zen-type SNP was remarkably high in the southern part of Japan, but low in the northern part. To examine the relationship between MFT-3A genotype and grain dormancy, we performed a germination assay in three wheat-growing seasons. On average, the varieties carrying the Zen-type SNP showed stronger grain dormancy than the varieties carrying the non-Zen-type SNP. Among commercial cultivars, ‘Iwainodaichi’ (Kyushu), ‘Junreikomugi’ (Kinki-Chugoku-Shikoku), ‘Kinuhime’ (Kanto-Tokai), ‘Nebarigoshi’ (Tohoku-Hokuriku), and ‘Kitamoe’ (Hokkaido) showed the strongest grain dormancy in each geographical group, and all these varieties, except for ‘Kitamoe’, were found to carry the Zen-type SNP. In recent years, the number of varieties carrying the Zen-type SNP has increased in the Tohoku-Hokuriku region, but not in the Hokkaido region.     

Expression of seed storage proteins responsible for maintaining kernel traits and wheat flour quality in common wheat under heat stress conditions

Heat stress during grain filling has been documented to decrease wheat grain yield and quality in arid regions worldwide. We studied the effect of heat stress on wheat flour quality in heat tolerant cultivars to define the effects of heat stress on flour quality and to identify germplasm combining traits for heat tolerance and good flour quality. We studied the kernel phenotypic traits, the expression of seed storage proteins (SSPs), and the resulting flour quality under heat and normal conditions. Under heat stress, all cultivars yielded narrow-shaped seeds, and increased protein contents as compared to the control plants grown under normal conditions. The specific sedimentation values used to estimate the gluten quality varied between cultivars. We identified cultivars that could maintain good flour quality under heat stress conditions: ‘Imam’, which possessed the Glu-D1d allele responsible for the suitable bread-making; ‘Bohaine’, which displayed high expression level of SSPs; and ‘Condor’, which possessed slight variations in the ratio of each SSP under heat stress conditions. Combining the desirable traits from these cultivars could yield a wheat cultivar with heat tolerance and good flour quality.     

春化、光周期和矮秆基因在不同国家小麦品种中的分布及其效应

为促进国外种质资源在我国的有效利用,将14个国家的100份代表性小麦品种在国内的8个代表性地点种植,调查抽穗期、成熟期和株高,并以4个春化基因(Vrn-A1、Vrn-B1、Vrn-D1和Vrn-B3)、1个光周期基因(Ppd-D1a)及2个矮秆基因(Rht-B1b和Rht-D1b)的分子标记检测所有品种的基因型。春化基因Vrn-A1a、Vrn-B1、Vrn-D1和vrn-A1+vrn-B1+ vrn-D1的分布频率分别为8.0%、21.0%、21.0%和64.0%;显性等位变异Vrn-A1a、Vrn-B1和Vrn-D1主要存在于来自中国春麦区及意大利、印度、加拿大、墨西哥和澳大利亚的品种中,这些品种一般为春性类型;春化位点均为隐性等位变异或vrn-A1+vrn-D1+Vrn-B1的品种主要分布在中国冬麦区、美国冬麦区、俄罗斯冬麦区,以及英国、法国、德国、罗马尼亚、土耳其和匈牙利,这些地区的小麦均为冬性类型。秋播时,供试品种均能正常抽穗,且携带春化显性变异的材料较隐性类型抽穗早,显性等位变异表现加性效应,4个春化位点均为隐性变异的一些欧美材料因抽穗太晚在杨凌和成都不能正常成熟;而春播时,显性等位变异基因型抽穗的频率高,隐性等位变异基因型基本不能抽穗。光周期不敏感基因Ppd-D1a的分布频率为68.0%,主要分布在中国、法国、罗马尼亚、俄罗斯、墨西哥、澳大利亚和印度,而光周期敏感等位变异Ppd-D1b主要分布在英国、德国、匈牙利和加拿大等中高纬度地区;携带Ppd-D1a的品种较携带Ppd-D1b的品种抽穗早,大多数Ppd-D1a品种在长日照和短日照条件下均能成熟,大部分Ppd-D1b品种在短日照条件下不能成熟。Rht-B1b和Rht-D1b基因的分布频率分别为43.0%和35.0%,其中Rht-B1b主要分布于美国、罗马尼亚、土耳其、意大利、墨西哥和澳大利亚,Rht-D1b主要分布于中国、德国、英国、意大利和印度。一般来说,一个国家的品种携带Rht-B1b或Rht-D1b之一,而这2个基因在高纬度地区分布频率较低。Rht-B1b、Rht-D1b和Ppd-D1a的降秆作用均达显著水平,Rht-B1b和Rht-D1b的加性效应突出。     

Identificaiton of a clubroot resistance locus conferring resistance to a Plasmodiophora brassicae classified into pathotype group 3 in Chinese cabbage (Brassica rapa L.)

In Chinese cabbage (Brassica rapa), the clubroot resistance (CR) genes Crr1 and Crr2 are effective against the mild Plasmodiophora brassicae isolate Ano-01 and the more virulent isolate Wakayama-01, but not against isolate No. 14, classified into pathotype group 3. ‘Akiriso’, a clubroot-resistant F₁ cultivar, showed resistance to isolate No. 14. To increase the durability of resistance, we attempted to identify the CR locus in ‘Akiriso’. CR in ‘Akiriso’ segregated as a single dominant gene and was linked to several molecular markers that were also linked to CRb, a CR locus from cultivar ‘CR Shinki’. We developed additional markers around CRb and constructed partial genetic maps of this region in ‘Akiriso’ and ‘CR Shinki’. The positions and order of markers in the genetic maps of the two cultivars were very similar. The segregation ratios for resistance to isolate No. 14 in F₂ populations derived from each of the two cultivars were also very similar. These results suggest that the CR locus in ‘Akiriso’ is CRb or a tightly linked locus. The newly developed markers in this study were more closely linked to CRb than previously reported markers and will be useful for marker-assisted selection of CRb in Chinese cabbage breeding.     

Leaf margin phenotype-specific restriction-site-associated DNA-derived markers for pineapple (Ananas comosus L.)

To explore genome-wide DNA polymorphisms and identify DNA markers for leaf margin phenotypes, a restriction-site-associated DNA sequencing analysis was employed to analyze three bulked DNAs of F1 progeny from a cross between a ‘piping-leaf-type’ cultivar, ‘Yugafu’, and a ‘spiny-tip-leaf-type’ variety, ‘Yonekura’. The parents were both Ananas comosus var. comosus. From the analysis, piping-leaf and spiny-tip-leaf gene-specific restriction-site-associated DNA sequencing tags were obtained and designated as PLSTs and STLSTs, respectively. The five PLSTs and two STSLTs were successfully converted to cleaved amplified polymorphic sequence (CAPS) or simple sequence repeat (SSR) markers using the sequence differences between alleles. Based on the genotyping of the F1 with two SSR and three CAPS markers, the five PLST markers were mapped in the vicinity of the P locus, with the closest marker, PLST1_SSR, being located 1.5 cM from the P locus. The two CAPS markers from STLST1 and STLST3 perfectly assessed the ‘spiny-leaf type’ as homozygotes of the recessive s allele of the S gene. The recombination value between the S locus and STLST loci was 2.4, and STLSTs were located 2.2 cM from the S locus. SSR and CAPS markers are applicable to marker-assisted selection of leaf margin phenotypes in pineapple breeding.     

Identification of a novel gene (Apq1) from the indica rice cultivar ‘Habataki’ that improves the quality of grains produced under high temperature stress

The appearance of brown rice grown under high temperature conditions is an important characteristic for improvement in Japanese rice breeding programs. We performed a QTL analysis of the appearance quality of brown rice using chromosome segment substitution lines of the indica cultivar ‘Habataki’ in the ‘Koshihikari’ genetic background. A line carrying a ‘Habataki’ segment on chromosome 7 showed a high percentage of perfect grains produced under high temperature conditions during the ripening period. To verify the role of this segment, and to narrow down the region containing the useful allele, substitution mapping was performed using multiple paired lines. As a result, the chromosomal location of a gene that we named Appearance quality of brown rice 1 (Apq1) was delimited to a 48-kb region. In addition, we developed an Apq1-near isogenic line (NIL) to evaluate the effect of Apq1 on various agronomic traits. Under high temperature conditions during the ripening period, the Apq1-NIL produced significantly higher percentages of perfect grains than ‘Koshihikari’. Other agronomic traits, including yield and palatability, were similar between the Apq1-NIL and ‘Koshihikari’. Therefore, the ‘Habataki’ allele of Apq1 will be useful in breeding programs aimed at improving the quality of grains ripened under high temperature conditions.     

The effect of drought stress on the leaf relative water content and tuber yield of a half-sib family of ‘Katahdin’-derived potato cultivars

Drought tolerance in plants is a complex trait involving morphological, physiological, and biochemical mechanisms. Hundreds of genes underlie the response of plants to the stress. For crops, selecting cultivars that can produce economically significant yields under drought is a priority. Potato (Solanum tuberosum L.) is considered as drought sensitive crop, although cultivar-dependent differences in tolerance have been described. Cultivar ‘Katahdin’ possesses many appropriate characteristics and is widely used for breeding purposes worldwide; it also has enhanced tolerance to drought stress. In this study, we evaluated cv. ‘Katahdin’ and a half-sib family of 17 Katahdin-derived cultivars for leaf relative water content (RWC) and tuber yield under drought stress. The yields of cultivars ‘Wauseon’, ‘Katahdin’, ‘Magura’, ‘Calrose’, and ‘Cayuga’ did not significantly decline under drought stress. Among these five, Wauseon exhibited the lowest reduction in both tuber yield and relative water content under water shortage. The data showed that ‘Wauseon’ is the most attractive cultivar for studies of molecular and physiological processes under drought and for potato breeding due to low yield losses that correspond with high RWC values. This cultivar can serve as a reservoir of potentially useful genes to develop cultivars with enhanced tolerance to this abiotic stress.     

Development of cultivar-specific DNA markers based on retrotransposon-based insertional polymorphism in Japanese pear

We developed retrotransposon-based insertional polymorphism (RBIP) markers based on the long terminal repeat (LTR) sequences of copia-like retrotransposon Ppcrt4 and flanking genome sequences, which were derived from 454 sequencing data from Japanese pear (Pyrus pyrifolia) ‘Hosui’. Out of 40 sequences including both LTR and flanking genome regions, we developed 22 RBIP markers and used them for DNA profiling of 80 pear cultivars: 64 Japanese, 10 Chinese (Pyrus ussuriensis) and 6 European (Pyrus communis). Three RBIP markers were enough to differentiate ‘Hosui’ from the other Japanese pear cultivars. The 22 RBIP markers could also distinguish 61 of the 64 Japanese pear cultivars. European pears showed almost no amplification of the 22 RBIP markers, which might suggest that retrotransposons had transposed during Asian pear evolution or reflect the genetic relationship between Asian and European pears. Sixteen of the RBIP markers could be positioned on a genetic linkage map of ‘Hosui’. The RBIP loci were distributed in 10 linkage groups, and some loci were very closely located within the same linkage group. The information obtained will be applicable to developing cultivar-specific RBIP marker sets in plants.     

Reverted glutathione S-transferase-like genes that influence flower color intensity of carnation (Dianthus caryophyllus L.) originated from excision of a transposable element

A glutathione S-transferase-like gene, DcGSTF2, is responsible for carnation (Dianthus caryophyllus L.) flower color intensity. Two defective genes, DcGSTF2mu with a nonsense mutation and DcGSTF2-dTac1 containing a transposable element dTac1, have been characterized in detail in this report. dTac1 is an active element that produces reverted functional genes by excision of the element. A pale-pink cultivar ‘Daisy’ carries both defective genes, whereas a spontaneous deep-colored mutant ‘Daisy-VPR’ lost the element from DcGSTF2-dTac1. This finding confirmed that dTac1 is active and that the resulting reverted gene, DcGSTF2rev1, missing the element is responsible for this color change. Crosses between the pale-colored cultivar ‘06-LA’ and a deep-colored cultivar ‘Spectrum’ produced segregating progeny. Only the deep-colored progeny had DcGSTF2rev2 derived from the ‘Spectrum’ parent, whereas progeny with pale-colored flowers had defective forms from both parents, DcGSTF2mu and DcGSTF2-dTac1. Thus, DcGSTF2rev2 had functional activity and likely originated from excision of dTac1 since there was a footprint sequence at the vacated site of the dTac1 insertion. Characterizing the DcGSTF2 genes in several cultivars revealed that the two functional genes, DcGSTF2rev1 and DcGSTF2rev2, have been used for some time in carnation breeding with the latter in use for more than half a century.     

Genetic region responsible for the differences of starch properties in two glutinous rice cultivars in Hokkaido,Japan

Starch properties are major determinants of grain quality and food characteristics in rice (Oryza sativa L.). Control of starch properties will lead to the development of rice cultivars with desirable characteristics. We performed quantitative trait locus analysis and detected a putative region on chromosome 2 associated with phenotypic variation of starch properties in two glutinous rice varieties developed in the Hokkaido region of Japan: ‘Kitayukimochi’, which has a low pasting temperature and creates soft rice cakes, and ‘Shirokumamochi’, which has a high pasting temperature and creates hard rice cakes. Starch branching enzyme IIb (SbeIIb) was identified as a candidate gene within the region. Sequence analysis of SbeIIb in parental lines identified two single-nucleotide polymorphisms (SNPs) with non-synonymous mutations in the coding region of the ‘Shirokumamochi’ genotype (SbeIIb^sr). We genotyped over 100 rice cultivars, including 28 rice varieties in the Honshu region of Japan, using the CAPS marker, which was designed using one of the SNPs. However, SbeIIb^sr was not found in rice cultivars in Honshu. Distribution analysis indicated that SbeIIb^sr was introduced to the rice breeding population in Hokkaido from the American variety ‘Cody’ via the Hokkaido cultivar ‘Kitaake’. As a result, SbeIIb^sr was distributed only in progenies of ‘Kitaake’.     

Genome-wide indel markers shared by diverse Asian rice cultivars compared to Japanese rice cultivar ‘Koshihikari’

Insertion-deletion (indel) polymorphisms, such as simple sequence repeats, have been widely used as DNA markers to identify QTLs and genes and to facilitate rice breeding. Recently, next-generation sequencing has produced deep sequences that allow genome-wide detection of indels. These polymorphisms can potentially be used to develop high-accuracy polymerase chain reaction (PCR)-based markers. Here, re-sequencing of 5 indica, 2 aus, and 3 tropical japonica cultivars and Japanese elite cultivar ‘Koshihikari’ was performed to extract regions containing large indels (10–51 bp) shared by diverse cultivars. To design indel markers for the discrimination of genomic regions between ‘Koshihikari’ and other diverse cultivars, we subtracted the indel regions detected in ‘Koshihikari’ from those shared in other cultivars. Two sets of indel markers, KNJ8-indel (shared in eight or more cultivars, including ‘Khao Nam Jen’ as a representative tropical japonica cultivar) and C5-indel (shared in five to eight cultivars), were established, with 915 and 9,899 indel regions, respectively. Validation of the two marker sets by using 23 diverse cultivars showed a high PCR success rate (≥95%) for 83.3% of the KNJ8-indel markers and 73.9% of the C5-indel markers. The marker sets will therefore be useful for the effective breeding of Japanese rice cultivars.     

Study on lily introgression breeding using allotriploids as maternal parents in interploid hybridizations

Based on a recent hypothesis, “Five same genomes of endosperm are essential for its development in Lilium”, it is expected that allotriploid lily (OTO) can be hybridized with diploid Oriental lily (OO) for introgression breeding in Lilium L.. To test the hypothesis, OTO lilies, ‘Belladonna’, ‘Candy Club’ and ‘Travatore’, were used as the maternal parents and crossed with two diploid OO cultivars, ‘Siberia’ and ‘Sorbonne’, and the species L. regale Wilson (TT). Results showed that capsules of all OTO × OO hybridizations developed well and 0.8~3.3 viable seedlings per ovary were obtained through normal pollination and embryo rescue; however, all OTO × TT crosses failed. Genomic in situ hybridization showed that the progenies of the OTO × OO hybridizations were aneuploid and a variable number of T-genome chromosomes were introduced into the progenies through the allotriploid lilies. The present results not only demonstrate that allotriploid OTO lilies, although male sterile, can be used as maternal parents to produce aneuploid progenies, but also strongly support the new hypothesis in lily breeding.     

Identification of quantitative trait loci associated with boiled seed hardness in soybean

Boiled seed hardness is an important factor in the processing of soybean food products such as nimame and natto. Little information is available on the genetic basis for boiled seed hardness, despite the wide variation in this trait. DNA markers linked to the gene controlling this trait should be useful in soybean breeding programs because of the difficulty of its evaluation. In this report, quantitative trait locus (QTL) analysis was performed to reveal the genetic factors associated with boiled seed hardness using a recombinant inbred line population developed from a cross between two Japanese cultivars, ‘Natto-shoryu’ and ‘Hyoukei-kuro 3’, which differ largely in boiled seed hardness, which in ‘Natto-shoryu’ is about twice that of ‘Hyoukei-kuro 3’. Two significantly stable QTLs, qHbs3-1 and qHbs6-1, were identified on chromosomes 3 and 6, for which the ‘Hyoukei-kuro 3’ alleles contribute to decrease boiled seed hardness for both QTLs. qHbs3-1 also showed significant effects in progeny of a residual heterozygous line and in a different segregating population. Given its substantial effect on boiled seed hardness, SSR markers closely linked to qHbs3-1, such as BARCSOYSSR_03_0165 and BARCSOYSSR_03_0185, could be useful for marker-assisted selection in soybean breeding.