Molecular breeding

About: Molecular breeding is a research topic. Over the lifetime, 2120 publications have been published within this topic receiving 56908 citations.

Citrus breeding, genetics and genomics in Japan.

Abstract: Citrus is one of the most cultivated fruits in the world, and satsuma mandarin (Citrus unshiu Marc.) is a major cultivated citrus in Japan. Many excellent cultivars derived from satsuma mandarin have been released through the improvement of mandarins using a conventional breeding method. The citrus breeding program is a lengthy process owing to the long juvenility, and it is predicted that marker-assisted selection (MAS) will overcome the obstacle and improve the efficiency of conventional breeding methods. To promote citrus molecular breeding in Japan, a genetic mapping was initiated in 1987, and the experimental tools and resources necessary for citrus functional genomics have been developed in relation to the physiological analysis of satsuma mandarin. In this paper, we review the progress of citrus breeding and genome researches in Japan and report the studies on genetic mapping, expression sequence tag cataloguing, and molecular characterization of breeding characteristics, mainly in terms of the metabolism of bio-functional substances as well as factors relating to, for example, fruit quality, disease resistance, polyembryony, and flowering.

In Vitro Plant Breeding

Abstract: Contents * Foreword * Preface * Chapter 1. Introduction * Types of In Vitro Culture * Applications of Plant Tissue Culture * Chapter 2. Morphogenesis/Organogenesis * Introduction * Plant Growth * Cellular Differentiation * Morphogenesis * Chapter 3. Micropropagation * Definition * Stages in Micropropagation * Commercial Micropropagation * Applications of Micropropagation * Chapter 4. Haploid Plant Production In Vitro * Anatomy of Anther * Anther Culture * Androgenesis * Chapter 5. In Vitro Pollination and Fertilization * Development of Female Gametophyte * Pollination * Fertilization * Embryo Culture * Chapter 6. Somatic Hybridization Using Protoplast Technology * Introduction * Uses of Protoplast Technology * Obtaining Protoplasts * The Culture of Protoplasts * The Cytoplasmic Genomes * Common Potential of Protoplast Fusion * Chapter 7. Cell Culture and Selection of Desirable Traits * Selection of Naturally Occurring Variants in Culture * General Selection Strategies * Chapter 8. In Vitro Mutagenesis * Types of Mutagens * Determining the Type and Suitable Concentration of Mutagens * The Choice of Plant Tissues for In Vitro Mutagensis * Chapter 9. The Origin, Nature, and Significance of Variation in Tissue Culture * Introduction * The Basis of Somaclonal Variations * Causes of Somaclonal Variations * Use of Somaclonal Variation in Breeding * Prevention of Somaclonal Variation * Chapter 10. Cryopreservation and Plant Breeding * Introduction * Theory and Technology * Cryopreservation Protocols for Cold-Hardy and Non-Cold-Hardy Species * Storage and Thawing * Equipment for Cryopreservation * Practical Issues and Strategies Toward Improved Cryoprotection * Chapter 11. In Vitro Micrografting * Definition of Micrografting * Analysis of Compatibility and Incompatibility Phenomena * Chapter 12. In Vitro Flowering: Its Relevance to Plant Breeding * Factors Influencing In Vitro Flowering * Plant Growth Regulators * Mineral Nutrients and Other Medium Components * Explant, Light, and Other Variables * Application of In Vitro Flowering to Plant Breeding * Chapter 13. In Vitro Tuberization * Introduction * Factors Controlling Microtuber Production * Practical Aspects of In Vitro Tuberization * Chapter 14. Molecular Plant Breeding * Types of Molecular Markers * Major Objectives of Molecular Breeding * Applications of Molecular Markers in Plant Breeding * Case Study: Application of Molecular Markers in Barley (Hordeum vulgare) Breeding * References * Index

Development of a core SNP arrays based on the KASP method for molecular breeding of rice

Abstract: The development and utilization of genetic markers play a pivotal role in marker-assisted breeding of rice cultivars during pyramiding of valuable genes. Among molecular markers, SNPs have become the most promising due to their wide distribution within genomes and suitability for high -throughput automated genotyping. Although metadata of SNPs have been identified via next generation sequencing in rice, a large gap between the development of SNP markers and the application in breeding still exists. To promote the application of SNP markers based on the KASP (Kompetitive Allele-Specific PCR) method in rice breeding, a set of core SNP arrays was built via the screening of SNP databases and literature resources based on the KASP method. Five hundred and ninety six SNPs classified into eight subsets including quality control, indica-indica variation, highly polymorphic, functional genes, key genes targeting sites, gene cloned region, important trait associated and gap filling sites were chosen to design KASP primers and 565 out of them were successfully designed, and the assay design success rate was 94.8%. Finally, 467 out of the 565 successfully-designed SNPs can display diversity at the loci were used to develop a set of core SNP arrays. To evaluate the application value of the core SNP markers in rice breeding, 481 rice germplasms were genotyped with three functional KASP markers designed from the sequences of GBSSI, SSIIa, and Badh2 from the core SNP arrays for estimation of their grain quality performance. Eighteen rice lines, including Xiangwanxian 13, Basmati 370, Ruanhua A, and PR 33319–9–1-1-5-3-5-4-1, harbor all three favorable alleles. The core KASP arrays were also used for rice germplasm assessment, genetic diversity and population evaluation. Four hundred and eighty-one rice germplasms were divided into 3 groups: POP1, POP2 and POP3. POP1 and POP2 were indica rice subgroups consisting of 263 and 186 rice germplasms, respectively. POP3 was a japonica rice subgroup consisting of 32 rice germplasms. The average FST value for the three subgroups was 0.3501; the FST value of POP1 and POP3 was the largest (0.5482), while that of POP1 and POP2 was the smallest (0.0721). The results showed that the genetic distance between the japonica and indica rice subspecies was large, indicating that the core SNP markers were effective at discriminating the population structure of the germplasms. Finally, the core KASP arrays were used for association analysis with milled grain traits. A total of 31 KASP markers were significantly associated (P < 0.01) with ML and the LWR. Among the 31 markers, 13 were developed based on cloned genes or on identified loci related to yield traits. Notably, several KASP markers associated with grain quality were also found to be associated with brown planthopper resistance or green leafhopper resistance simultaneously. The core KASP arrays developed in our study were efficient and versatile for rice germplasm assessment, genetic diversity and population evaluation and are valuable for promoting SNP molecular breeding in rice. Our study demonstrated that useful assays combined with molecular breeding can be exploited for important economic trait improvement in rice breeding.

Impact of Molecular Technologies on Faba Bean (Vicia faba L.) Breeding Strategies

Abstract: Faba bean (Vicia faba L.) is a major food and feed legume because of the high nutritional value of its seeds. The main objectives of faba bean breeding are to improve yield, disease resistance, abiotic stress tolerance, seed quality and other agronomic traits. The partial cross-pollinated nature of faba bean introduces both challenges and opportunities for population development and breeding. Breeding methods that are applicable to self-pollinated crops or open-pollinated crops are not highly suitable for faba bean. However, traditional breeding methods such as recurrent mass selection have been established in faba bean and used successfully in breeding for resistance to diseases. Molecular breeding strategies that integrate the latest innovations in genetics and genomics with traditional breeding strategies have many potential applications for future faba bean cultivar development. Hence, considerable efforts have been undertaken in identifying molecular markers, enriching genetic and genomic resources using high-throughput sequencing technologies and improving genetic transformation techniques in faba bean. However, the impact of research on practical faba bean breeding and cultivar release to farmers has been limited due to disconnects between research and breeding objectives and the high costs of research and implementation. The situation with faba bean is similar to other small crops and highlights the need for coordinated, collaborative research programs that interact closely with commercially focused breeding programs to ensure that technologies are implemented effectively.

MBKbase for rice: an integrated omics knowledgebase for molecular breeding in rice.

Abstract: To date, large amounts of genomic and phenotypic data have been accumulated in the fields of crop genetics and genomic research, and the data are increasing very quickly. However, the bottleneck to using big data in breeding is integrating the data and developing tools for revealing the relationship between genotypes and phenotypes. Here, we report a rice sub-database of an integrated omics knowledgebase (MBKbase-rice, www.mbkbase.org/rice), which integrates rice germplasm information, multiple reference genomes with a united set of gene loci, population sequencing data, phenotypic data, known alleles and gene expression data. In addition to basic data search functions, MBKbase provides advanced web tools for genotype searches at the population level and for visually displaying the relationship between genotypes and phenotypes. Furthermore, the database also provides online tools for comparing two samples by their genotypes and finding target germplasms by genotype or phenotype information, as well as for analyzing the user submitted SNP or sequence data to find important alleles in the germplasm. A soybean sub-database is planned for release in 3 months and wheat and maize will be added in 1-2 years. The data and tools integrated in MBKbase will facilitate research in crop functional genomics and molecular breeding.