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1.
Metabolites play a central role in maintaining organismal life and in defining crop phenotypes, such as nutritional value, fragrance, color, and stress resistance. Among the ‘omes’ in biology, the metabolome is the closest to the phenotype. Consequently, metabolomics has been applied to crop improvement as method for monitoring changes in chemical compositions, clarifying the mechanisms underlying cellular functions, discovering markers and diagnostics, and phenotyping for mQTL, mGWAS, and metabolite-genome predictions. In this review, 359 reports of the most recent applications of metabolomics to plant breeding-related studies were examined. In addition to the major crops, more than 160 other crops including rare medicinal plants were considered. One bottleneck associated with using metabolomics is the wide array of instruments that are used to obtain data and the ambiguity associated with metabolite identification and quantification. To further the application of metabolomics to plant breeding, the features and perspectives of the technology are discussed.  相似文献   

2.
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.  相似文献   

3.
Phenomics or automated phenotyping (AP) is an emerging approach, identified as a priority for future crop breeding research. This approach promises to provide accurate, precise, fast, large-scale, and accumulated phenotyping data which when integrated with corresponding genomic and environmental data is expected to trigger a great leap forward in plant breeding. However, despite promising applications, AP adoption in plant breeding is still in its infancy. It is unclear to many plant breeders how or if much of the enormous volume, diversity, and velocity of imaging and remote-sensing data generated by AP is going to be usefully integrated into breeding programs. This paper develops an economical model of heterogeneous breeders’ decision-making to examine adoption decisions regarding whether to adopt AP or continue using conventional phenotyping. The results of this model indicate that many interlocking factors, including genetic gain/expected return, variable and sunk costs, subsequent rate of technology improvement, and breeders’ level of aversion to AP, are at work as breeders determine whether to adopt AP. This study also provides a numerical example to show the impact of breeders’ aversion toward the adoption of a new technology (e.g., AP) on the expected return generated from breeding a new wheat variety.  相似文献   

4.
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5.
Smut disease of sugarcane causes considerable yield losses and the use of resistant varieties is the best control practice. Our group identified a Japanese wild sugarcane with highly smut disease resistance named ‘Iriomote8’. In this study, we conducted QTL analysis for smut disease resistance using a mapping population derived from a resistant variety ‘Yaenoushie’, in which resistance is inherited from ‘Iriomote8’. We identified 4813 non-redundant markers using GRAS-Di technology and developed a linkage map of mapping parents. We evaluated smut disease resistance of the mapping population by the inoculation test. Consequently, a large number of clones did not show the disease symptoms and the distribution of smut disease incidence tended to be “L shaped”. Composite interval mapping detected an identical QTL for indices of smut disease incidence with a markedly high LOD score (26.6~45.6) at the end of linkage group 8 of ‘Yaenoushie’. This QTL explained approximately 50% of the cases of smut disease incidence. In the mapping population, there were no correlations between the indices of smut disease incidence and other agronomic traits. In conclusion, this QTL could be used for marker-assisted selection to significantly improve smut disease resistance without negative effects on other agronomic traits.  相似文献   

6.
We developed 18 polymorphic simple sequence repeat (SSR) markers in pineapple (Ananas comosus) by using genomic libraries enriched for GA and CA motifs. The markers were used to genotype 31 pineapple accessions, including seven cultivars and 11 breeding lines from Okinawa Prefecture, 12 foreign accessions and one from a related species. These SSR loci were highly polymorphic: the 31 accessions contained three to seven alleles per locus, with an average of 4.1. The values of expected heterozygosity ranged from 0.09 to 0.76, with an average of 0.52. All 31 accessions could be successfully differentiated by the 18 SSR markers, with the exception of ‘N67-10’ and ‘Hawaiian Smooth Cayenne’. A single combination of three markers TsuAC004, TsuAC010 and TsuAC041, was enough to distinguish all accessions with one exception. A phenogram based on the SSR genotypes did not show any distinct groups, but it suggested that pineapples bred in Japan are genetically diversed. We reconfirmed the parentage of 14 pineapple accessions by comparing the SSR alleles at 17 SSR loci in each accession and its reported parents. The obtained information will contribute substantially to protecting plant breeders’ rights.  相似文献   

7.
In contrast to high-throughput genotyping which can manage a large number of plants at relatively low cost, phenotyping of many individual genotypes in field trials is still laborious and expensive. Early plant vigour, as an early selection criterion, is a trait that is visually scored due to a lack of suitable phenotyping methods for an accurate detection of this trait in large field trials. A high-throughput phenotyping technique for scoring early plant vigour would enhance the breeding process. This study was conducted to develop a method for scoring phenotypic differences in early plant vigour of 50 winter wheat (Triticum aestivum L.) cultivars in a 2-years experiment using a vehicle based multispectral active sensor and two commercially available active sensors, GreenSeeker and CropCircle. Pixel analysis of RGB images revealed to be the most feasible and superior method compared to other possible reference methods. A comparison between the two years 2011 and 2012 confirmed that early plant vigour was affected by genotypic differences. A novel spectral plant vigour index (EPVI) was found to accurately reflect the plant vigour at tillering. Different methods were applied to identify optimal combinations of wavelengths to predict early plant vigour, including multivariate modelling and prediction, contour maps for identifying all possible simple ratios and testing of combined indices. The EPVI and the relative amount of green pixels (RAGP) derived from digital images were significantly related with r2 = 0.98 to each other in both years. A total of 200 plots, 12 m in length, could be measured within 75 min. The EPVI was shown to be an accurate scoring method for the high-throughput screening of large field trials. The rapidity and accuracy of this novel method may contribute to enhanced selection at early growth stages.  相似文献   

8.
Root system architecture (RSA) determines unevenly distributed water and nutrient availability in soil. Genetic improvement of RSA, therefore, is related to crop production. However, RSA phenotyping has been carried out less frequently than above-ground phenotyping because measuring roots in the soil is difficult and labor intensive. Recent advancements have led to the digitalization of plant measurements; this digital phenotyping has been widely used for measurements of both above-ground and RSA traits. Digital phenotyping for RSA is slower and more difficult than for above-ground traits because the roots are hidden underground. In this review, we summarized recent trends in digital phenotyping for RSA traits. We classified the sample types into three categories: soil block containing roots, section of soil block, and root sample. Examples of the use of digital phenotyping are presented for each category. We also discussed room for improvement in digital phenotyping in each category.  相似文献   

9.
The whiteness of cooked rice and rice cakes was evaluated using a portable spectrophotometer with a whiteness index (WI). Also, by using boiled rice for measurement of Mido values by Mido Meter, it was possible to infer the whiteness of cooked rice without rice cooking. In the analysis of varietal differences of cooked rice, ‘Tsuyahime’, ‘Koshihikari’ and ‘Koshinokaori’ showed high whiteness, while ‘Satonoyuki’ had inferior whiteness. The whiteness of rice cakes made from ‘Koyukimochi’ and ‘Dewanomochi’ was higher than the whiteness of those made from ‘Himenomochi’ and ‘Koganemochi’. While there was a significant correlation (r = 0.84) between WI values and whiteness scores of cooked rice by the sensory test, no correlation was detected between the whiteness scores and Mido values, indicating that the values obtained by a spectrophotometer differ from those obtained by a Mido Meter. Thus, a spectrophotometer may be a novel device for measurement of rice eating quality.  相似文献   

10.
C. Dayteg    S. Tuvesson    A. Merker    A. Jahoor    A. Kolodinska-Brantestam   《Plant Breeding》2007,126(4):410-415
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11.
“Breeding by Design” as a concept described by Peleman and van der Voort aims to bring together superior alleles for all genes of agronomic importance from potential genetic resources. This might be achievable through high-resolution allele detection based on precise QTL (quantitative trait locus/loci) mapping of potential parental resources. The present paper reviews the works at the Chinese National Center for Soybean Improvement (NCSI) on exploration of QTL and their superior alleles of agronomic traits for genetic dissection of germplasm resources in soybeans towards practicing “Breeding by Design”. Among the major germplasm resources, i.e. released commercial cultivar (RC), farmers’ landrace (LR) and annual wild soybean accession (WS), the RC was recognized as the primary potential adapted parental sources, with a great number of new alleles (45.9%) having emerged and accumulated during the 90 years’ scientific breeding processes. A mapping strategy, i.e. a full model procedure (including additive (A), epistasis (AA), A × environment (E) and AA × E effects), scanning with QTLNetwork2.0 and followed by verification with other procedures, was suggested and used for the experimental data when the underlying genetic model was usually unknown. In total, 110 data sets of 81 agronomically important traits were analyzed for their QTL, with 14.5% of the data sets showing major QTL (contribution rate more than 10.0% for each QTL), 55.5% showing a few major QTL but more small QTL, and 30.0% having only small QTL. In addition to the detected QTL, the collective unmapped minor QTL sometimes accounted for more than 50% of the genetic variation in a number of traits. Integrated with linkage mapping, association mappings were conducted on germplasm populations and validated to be able to provide complete information on multiple QTL and their multiple alleles. Accordingly, the QTL and their alleles of agronomic traits for large samples of RC, LR and WS were identified and then the QTL-allele matrices were established. Based on which the parental materials can be chosen for complementary recombination among loci and alleles to make the crossing plans genetically optimized. This approach has provided a way towards breeding by design, but the accuracy will depend on the precision of the loci and allele matrices.  相似文献   

12.
Genome sequence analysis in higher plants began with the whole-genome sequencing of Arabidopsis thaliana. Owing to the great advances in sequencing technologies, also known as next-generation sequencing (NGS) technologies, genomes of more than 400 plant species have been sequenced to date. Long-read sequencing technologies, together with sequence scaffolding methods, have enabled the synthesis of chromosome-level de novo genome sequence assemblies, which has further allowed comparative analysis of the structural features of multiple plant genomes, thus elucidating the evolutionary history of plants. However, the quality of the assembled chromosome-level sequences varies among plant species. In this review, we summarize the status of chromosome-level assemblies of 114 plant species, with genome sizes ranging from 125 Mb to 16.9 Gb. While the average genome coverage of the assembled sequences reached up to 89.1%, the average coverage of chromosome-level pseudomolecules was 73.3%. Thus, further improvements in sequencing technologies and scaffolding, and data analysis methods, are required to establish gap-free telomere-to-telomere genome sequence assemblies. With the forthcoming new technologies, we are going to enter into a new genomics era where pan-genomics and the >1,000 or >1 million genomes’ project will be routine in higher plants.  相似文献   

13.
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.  相似文献   

14.
W. Erskine  J. Isawi  K. Masoud 《Euphytica》1990,48(2):113-116
Summary Individual plant selection for yield in lentil is problematic at a commercial crop density primarily because of inter-plant entanglement by tendrils. Visual plant selection for yield was compared with random selection in the F5 at three plant densities (66, 133 and 200 seeds/m2) by an evaluation of F7 progeny yields over two seasons in two populations of lentil. Random plant sampling was as effective as visual plant selection in isolating high-yielding F7 lines. The plant density of the selection environment did not affect the response to selection. The correlations between the seed number of selected F5 plants and the mean yield of their F7 progenies were r=+–0.26 and –0.06 in two populations, indicating the lack of positive response to plant selection for seed number. The results show that 1) random sampling is the most economic of the methods tested of plant selection for yield and 2) the plant density of the environment for plant selection can be low enough to avoid inter-plant entanglement by tendrils, allowing a focus in plant selection on characters, other than yield, of importance to the breeding program and with a higher heritability than yield.  相似文献   

15.
The objective of the National BioResource Project (NBRP) in Japan is to collect, conserve and distribute biological materials for life sciences research. The project consists of twenty-eight bioresources, including animal, plant, microorganism and DNA resources. NBRP Lotus and Glycine aims to support the development of legume research through the collection, conservation, and distribution of these bioresources. Lotus japonicus is a perennial legume that grows naturally throughout Japan and is widely used as a model plant for legumes because of such advantages as its small genome size and short life cycle. Soybean (Glycine max) has been cultivated as an important crop since ancient times, and numerous research programs have generated a large amount of basic research information and valuable bioresources for this crop. We have also developed a “LegumeBase” a specialized database for the genera Lotus and Glycine, and are maintaining this database as a part of the NBRP. In this paper we will provide an overview of the resources available from the NBRP Lotus and Glycine database site, called “LegumeBase”.  相似文献   

16.
Rice (Oryza sativa L.) is the main food for people in Laos, where it has been grown and eaten since prehistory. Diverse landraces are grown in Laos. ‘Khao Kai Noi’, a landrace favored for its eating quality, is held in the nationwide collection of traditional landraces in the Lao national genebank. Genetic diversity is crucial for sustainable use of genetic resources and conservation. To investigate the genetic diversity of ‘Khao Kai Noi’ for conservation, we genotyped 70 accessions by using 23 polymorphic simple sequence repeat markers. The markers generated 2 to 17 alleles (132 in total), with an average of 5.7 per locus. The total expected heterozygosity over all ‘Khao Kai Noi’ accessions was 0.271. Genetic variation was largest among accessions and smallest within accessions. Khao Kai Noi accessions were classified into three different genetic backgrounds, but there was unclear association between the three inferred population and name subgroups and geographical distribution. Most of the accessions were clustered with temperate japonica and showed genetic relatedness to rice from neighboring provinces of Vietnam, suggesting a Vietnamese origin. The results of this study will contribute to the conservation, core collection and future breeding of the Khao Kai Noi population.  相似文献   

17.
To develop a high density linkage map in faba bean, a total of 1,363 FBES (Faba bean expressed sequence tag [EST]-derived simple sequence repeat [SSR]) markers were designed based on 5,090 non-redundant ESTs developed in this study. A total of 109 plants of a ‘Nubaria 2’ × ‘Misr 3’ F2 mapping population were used for map construction. Because the parents were not pure homozygous lines, the 109 F2 plants were divided into three subpopulations according to the original F1 plants. Linkage groups (LGs) generated in each subpopulation were integrated by commonly mapped markers. The integrated ‘Nubaria 2’ × ‘Misr 3’ map consisted of six LGs, representing a total length of 684.7 cM, with 552 loci. Of the mapped loci, 47% were generated from multi-loci diagnostic (MLD) markers. Alignment of homologous sequence pairs along each linkage group revealed obvious syntenic relationships between LGs in faba bean and the genomes of two model legumes, Lotus japonicus and Medicago truncatula. In a polymorphic analysis with ten Egyptian faba bean varieties, 78.9% (384/487) of the FBES markers showed polymorphisms. Along with the EST-SSR markers, the dense map developed in this study is expected to accelerate marker assisted breeding in faba bean.  相似文献   

18.
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.  相似文献   

19.
Cooked rice of ‘Sasanishiki’ is soft and not as sticky as those of Japanese leading cultivars ‘Koshihikari’ and ‘Hitomebore’. As a method for efficient selection of a breeding line having a good eating quality like that of ‘Sasanishiki’, the use of physical properties of cooked rice and cooking quality was examined. There were differences of physical properties of the surface layer, starch-iodine blue value per solid substance weight in cooking water and volume expansion of cooked rice between ‘Sasanishiki’ and ‘Hitomebore’, these properties being considered to be usable for the selection of breeding lines. Using these traits as selection targets, one line, named ‘Tohoku 194’, which has eating quality highly similar to that of ‘Sasanishiki’ and cold tolerance derived from ‘Hitomebore’, was selected from progeny of a cross between ‘Sasanishiki’ and ‘Hitomebore’. An application for registration as a new variety has been submitted for ‘Tohoku 194’ under the Japanese Plant Variety Protection Act, and is expected to become a recommended cultivar in Miyagi Prefecture. ‘Tohoku 194’ may fulfill various demands of consumers and companies in the food industry.  相似文献   

20.
As plants cannot relocate, they require effective root systems for water and nutrient uptake. Root development plasticity enables plants to adapt to different environmental conditions. Research on improvements in crop root systems is limited in comparison with that in shoots as the former are difficult to image. Breeding more effective root systems is proposed as the “second green revolution”. There are several recent publications on root system architecture (RSA), but the methods used to analyze the RSA have not been standardized. Here, we introduce traditional and current root-imaging methods and discuss root structure phenotyping. Some important root structures have not been standardized as roots are easily affected by rhizosphere conditions and exhibit greater plasticity than shoots; moreover, root morphology significantly varies even in the same genotype. For these reasons, it is difficult to define the ideal root systems for breeding. In this review, we introduce several types of software to analyze roots and identify important root parameters by modeling to simplify the root system characterization. These parameters can be extracted from photographs captured in the field. This modeling approach is applicable to various legacy root data stored in old or unpublished formats. Standardization of RSA data could help estimate root ideotypes.  相似文献   

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