Soil flooding or waterlogging is a major abiotic stress in upland crops. In barley, there have been several reported studies of selection for flooding-tolerant genotypes, but it is difficult to obtain varietal rankings that are consistent among researchers. Our objectives were to establish experimental conditions that could be applied by other research groups and to verify the varietal ranking conducted in an earlier study. We conducted greenhouse experiments on 14 barley varieties. At the 2.5-leaf stage, they were flooded with 0% or 0.1% soluble starch solution (mimicking reducing conditions). At 13 to 15 days after the start of treatment, the degree of leaf injury and the shoot dry weight ratio (treatment:control) were recorded. Reliable and highly repeatable results were obtained for the criterion of leaf injury under reducing conditions, whereas shoot dry weight ratio was unstable. The varieties OUJ820 and OUA301 were highly tolerant, whereas OUA002 and OUJ247 were sensitive; these results matched those of the earlier study. The experimental conditions that we developed here may be useful for selection testing and genetic analysis of flooding tolerance in other laboratories.
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.
Total spikelet number per panicle (TSN) is one of the most important traits associated with rice yield potential. This trait was assessed in a set of 334 chromosomal segment introgression lines (ILs: BC3-derived lines), developed from new plant type (NPT) varieties as donor parents and having the genetic background of an indica-type rice variety IR64. Among the 334 ILs, five lines which had different donor parents and showed significantly higher TSN than IR64 were used for genetic analysis. Quantitative trait locus (QTL) analysis was conducted using F2 populations derived from crosses between IR64 and these ILs. As a result, a QTL for high TSN (one from each NPT donor variety) was detected on common region of the long arm of chromosome 4. The effect of the QTL was confirmed by an increase in TSN of five near-isogenic lines (NILs) developed in the present study. The variation in TSN was found among these NILs, attributing to the panicle architecture in the numbers of primary, secondary and tertiary branches. The NILs for TSN and the SSR markers linked to the TSN QTLs are expected to be useful materials for research and breeding to enhance the yield potential of rice varieties.
A total of 18 rainfed upland New Rice for Africa (NERICA) varieties were categorized as the heavy panicle and low tillering types and early heading, in compared with 32 different varieties. These chromosome components were clarified using 243 SSR markers which showed polymorphism among NERICA varieties and their parents, CG 14 (O. glaberrima Steud.) and one of the recurrent parents, WAB-56-104 (O. sativa L.). NERICA varieties were classified into three groups, which corresponded with these parents’ continuation including two exceptions, NERICAs 14 and 17, by a cluster analysis using polymorphism data of SSR markers and 14 differential markers among them were selected to classify NERICA varieties. However, three groups: NERICAs, 3 and 4, NERICAs, 8, 9 and 11 and NERICAs, 15 and 16 were not distinguishable. Association analysis was carried out for characterization of NERICA varieties by using SSR markers genotype and phenotype of agronomic traits. A total of 131 quantitative trait loci between SSR markers and 11 agronomic traits were detected. The characteristics of early maturity and heavy panicle of upland NERICA varieties were succeeded from Asian rice varieties and the characteristics of high dry matter production and late heading were introduced from CG 14 and the other varieties.
Aegilops tauschii Coss. is the D-genome donor to hexaploid bread wheat (Triticum aestivum) and is the most promising wild species as a genetic resource for wheat breeding. To study the population structure and diversity of 81 Ae. tauschii accessions collected from various regions of its geographical distribution, the genomic representation of these lines were used to develop a diversity array technology (DArT) marker array. This Ae. tauschii array and a previously developed DArT wheat array were used to scan the genomes of the 81 accessions. Out of 7500 markers (5500 wheat and 2000 Ae. tauschii), 4449 were polymorphic (3776 wheat and 673 Ae. tauschii). Phylogenetic and population structure studies revealed that the accessions could be divided into three groups. The two Ae. tauschii subspecies could also be separately clustered, suggesting that the current taxonomy might be valid. DArT markers are effective to detect very small polymorphisms. The information obtained about Ae. tauschii in the current study could be useful for wheat breeding. In addition, the new DArT array from this Ae. tauschii population is expected to be an effective tool for hexaploid wheat studies.
Expression of MdACS3a, one of the ripening-related ACC synthase genes, plays a pivotal role in initiating the burst of ethylene production by MdACS1 in apple fruit. Although previous studies have demonstrated the presence of MdACS3a-null alleles through deficiency of transcription activity or loss of enzyme activity due to amino acid substitution, which may affect the storage properties of certain fruit cultivars, an overall picture of these null alleles in cultivars is still lacking. The present study investigated the distribution of null allelic genes in 103 cultivars and 172 breeding selections by using a simple sequence repeat (SSR) marker linked to them. The results indicated that both allelic genes were widely distributed throughout the examined cultivars and selections, some occurring as the null genotype, either homozygously or heterozygously, with each null allele. The implications of MdACS3a distribution results and the influence of its null allelotypes in fruit characters are discussed.
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.
To reveal varietally differing glucosinolate (GSL) contents in radish (Raphanus sativus L.) cultivated in Japan, the total and individual GSLs of 28 cultivars were analyzed using high-performance liquid chromatography. In these cultivars, GSL types including three aliphatic GSLs (glucoraphenin, glucoerucin, and 4-methylthio-3-butenyl GSL (4MTB-GSL)) and three indolyl GSLs (4-hydroxy-glucobrassicin, glucobrassicin, and 4-methoxy-glucobrassicin) were detected. No cultivar-specific type of GSL was identified. The dominant GSL was 4MTB-GSL, but its contents differed remarkably: 8.6 μmol/g in ‘Koushin’ to 135.7 μmol/g in ‘Karami 199’. Over about 90% of all GSLs in Japanese radish type are 4MTB-GSL, a higher percentage than in Chinese or European garden radish cultivars. A simple, rapid method for estimating total GSL contents in crude extracts was established because of the small variation of glucosinolate composition in Japanese cultivars. The total GSL content can be estimated using an equation for prediction with absorbance at 425 nm in a mixture of GSL crude extract and palladium (II) chloride solution: Total GSL (μmol/g) = 305.47 × A425 − 29.66. Its coefficient of determination (R2) and standard error of prediction (SEP) are 0.968 and 8.052. This method enables total GSL content estimation from more than 200 samples per person per day.
Five physiological and eleven yield traits of two pairs of sister lines generated from a high generation with similar genetic background (SLs) for purple pericarp were investigated to explore the reasons behind low-yield production of colored rice. Of the five physiological traits examined, except grain anthocyanin content, there were generally similar trends between the P (purple-pericarp) lines and the corresponding W (white-pericarp) lines over two seasons (in the year 2009 and 2010 separately). The results demonstrated that the chlorophyll content of flag leaves, the net photosynthetic rate of flag leaves, and the grain anthocyanin content could be easily influenced by the environment. The physiological functions of the traits for the P lines were more active than those of the corresponding W lines in the year 2010. The grain anthocyanin content of the P lines was much greater in the year 2010 than in the year 2009 during the growth period. The investigation of yield traits revealed that the P lines had reduced 1000-grain weight, yield per plot and grain/brown rice thickness compared to the W lines. A difference comparison of these traits and a source-sink and transportation relationship analysis for these SLs suggested that small sink size was a key reason behind yield reduction of purple pericarp rice.
The tolerance of the dune grass Leymus mollis (Triticeae; Poaceae) to various biotic and abiotic stresses makes it a very useful genetic resource for wheat breeding. Wide hybridization between L. mollis and wheat allows the introduction of Leymus chromosomes into the wheat genetic background and facilitates the integration of useful traits into wheat. However, the genetic basis controlling the physiological tolerance of L. mollis to multiple environmental stresses remains largely unexplored. Using suppression subtractive hybridization, we identified 112 osmotic-stress-responsive genes from L. mollis and confirmed their differential expression under osmotic stress. These genes were categorized into 13 functional categories, including cell defense and stress response, transcriptional regulation, signal transduction, biosynthesis of compatible solutes and cell wall metabolism. Representative genes were validated by northern blot and RT-PCR analyses of expression patterns in response to osmotic stress and abscisic acid treatment. The genes identified here represent a useful source of expressed sequence tags (ESTs) for the analysis and identification of Leymus chromosomes introduced into wheat. Furthermore, being highly conserved, genetically associated with osmotic stress tolerance and transferable to wheat, these ESTs provide significant tools for the development of EST-derived molecular markers for introgression of osmotic stress tolerance genes into wheat.
Phytic acid (PA) is the storage form of phosphorus (P) in seeds and plays an important role in the nutritional quality of food crops. There is little information on the genetics of seed and seedling PA in mungbean [Vigna radiata (L.) Wilczek]. Quantitative trait loci (QTL) were identified for phytic acid P (PAP), total P (TP), and inorganic P (IP) in mungbean seeds and seedlings, and for flowering, maturity and seed weight, in an F2 population developed from a cross between low PAP cultivated mungbean (V1725BG) and high PAP wild mungbean (AusTRCF321925). Seven QTLs were detected for P compounds in seed; two for PAP, four for IP and one for TP. Six QTLs were identified for P compounds in seedling; three for PAP, two for TP and one for IP. Only one QTL co-localized between P compounds in seed and seedling suggesting that low PAP seed and low PAP seedling must be selected for at different QTLs. Seed PAP and TP were positively correlated with days to flowering and maturity, indicating the importance of plant phenology to seed P content.
Of the Capsicum peppers (Capsicum spp.), cultivated C. annuum is the most commercially important, but has lacked an intraspecific linkage map based on sequence-specific PCR markers in accord with haploid chromosome numbers. We constructed a linkage map of pepper using a doubled haploid (DH) population derived from a cross between two C. annuum genotypes, a bell-type cultivar ‘California Wonder’ and a Malaysian small-fruited cultivar ‘LS2341 (JP187992)’, which is used as a source of resistance to bacterial wilt (Ralstonia solanacearum). A set of 253 markers (151 SSRs, 90 AFLPs, 10 CAPSs and 2 sequence-tagged sites) was on the map which we constructed, spanning 1,336 cM. This is the first SSR-based map to consist of 12 linkage groups, corresponding to the haploid chromosome number in an intraspecific cross of C. annuum. As this map has a lot of PCR-based anchor markers, it is easy to compare it to other pepper genetic maps. Therefore, this map and the newly developed markers will be useful for cultivated C. annuum breeding.
Although Japanese morning glory (Ipomoea nil (L.) Roth.) has been used intensively for genetic studies, DNA markers have not been developed in Ipomoea nil sufficient to cover all chromosomes. Therefore, we conducted microsatellite (simple sequence repeats, SSR) marker development in I. nil for future genetic studies. From 92,662 expressed sequence tag (EST) sequences, 514 unique microsatellite-containing ESTs were identified. Primer pairs were designed automatically in 326 SSRs. Of 150 SSRs examined, 75 showed polymorphisms among strains. A phenogram based on the SSR genotypes revealed the genetic relation among seven Japanese morning glories from five different regions of the world and an ivyleaf morning glory (I. hederacea Jacq.). The developed SSR markers might be applicable for genetic studies of morning glories and their relatives.