Molecular breeding

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

Exploiting the Genomic Diversity of Rice (Oryza sativa L.): SNP-Typing in 11 Early-Backcross Introgression-Breeding Populations

Abstract: This study demonstrates genotyping-by-sequencing-based single-nucleotide polymorphism (SNP)-typing in 11 early-backcross introgression populations of rice (at BC1F5), comprising a set of 564 diverse introgression lines and 12 parents. Sequencing using 10 Ion Proton runs generated a total of ∼943.4 million raw reads, out of which ∼881.6 million reads remained after trimming for low-quality bases. After alignment, 794,297 polymorphic SNPs were identified, and filtering resulted in LMD50 SNPs (low missing data, with each SNP, genotyped in at least 50% of the samples) for each sub-population. Every data point was supported by actual sequencing data without any imputation, eliminating imputation-induced errors in SNP calling. Genotyping substantiated the impacts of novel breeding strategy revealing: (a) the donor introgression patterns in ILs were characteristic with variable introgression frequency in different genomic regions, attributed mainly to stringent selection under abiotic stress and (b) considerably lower heterozygosity was observed in ILs. Functional annotation revealed 426 non-synonymous deleterious SNPs present in 102 loci with a range of 1-4 SNPs per locus and 120 novel SNPs. SNP-typing this diversity panel will further assist in the development of markers supporting genomic applications in molecular breeding programs.

Molecular genetics and breeding of vegetable brassicas

Abstract: Genetic traits relevant to breeding vegetable brassicas are surveyed to determine the effects that recent advances in molecular genetics and molecular marker technology might have on breeding priorties and practices. The problems peculiar to breeding horticultural crops are addressed. The application of DNA restriction fragment length polymorphisms (RFLPs) as an aid to breeding brassicas is discussed and genes amenable to molecular analysis are considered in the light of both experimental and economic factors.

Kultur Antera untuk Percepatan Perakitan Varietas Padi di Indonesia

Abstract: Rice is a staple food crop in Indonesia, while the need is increasing due to high rice consumption as well as population increase. The problems can be solved through increase of national rice production. Productivity of lowland and upland should be increased intensively and other potential dry area outside Java and Bali Islands should be considered for extending the area of production. Recently, high yielding variety such as semi dwarf variety, hybrid rice, and new plant type of rice were being developed by Indonesian breeders. However, new method is needed to complement conventional breeding method in order to accelerate rice breeding. Anther culture is one of in vitro culture techniques that can be used to accelerate the obtainment of pure lines through doubled-haploids (DHs) regenerated at first generation of culture for less than one year. Thus, application of anther culture in conventional breeding will increase the efficiency of selection process as well as reducing the cost for labour, land and breeder’s time. The obtainment of green plantlets derived from anther culture of indica rice subspecies has been improved by the addition of 1 mM putrescine into induction and regeneration media. Recently, several upland rice lines tolerant to abiotic stresses (i.e. low light intensity and aluminum toxicity) and biotic stresses (i.e. leaf and neck blast), several lowland rice/paddy lines tolerant to biotic stresses (i.e. bacterial leaf blight and blast), and several hybrid parental lines (i.e. male sterile, maintainer and restorer) were obtained in 2-3 years from several rice breeding program involving anther culture. However, potential use anther culture to provide unique genetic material for mapping populations for use in functional genomics and molecular breeding has not been explored. The results indicated that anther culture is a feasible technology that can be used for accelerating rice breeding program in Indonesia.

Exploration of rice yield potential: Decoding agronomic and physiological traits

Abstract: Rice grain yield is determined by three major “visible” morphological traits: grain weight, grain number per panicle, and effective tiller number, which are affected by a series of “invisible” physiological factors including nutrient use efficiency and photosynthetic efficiency. In the past few decades, substantial progress has been made on elucidating the molecular mechanisms underlying grain yield formation, laying a solid foundation for improving rice yield by molecular breeding. This review outlines our current understanding of the three morphological yield-determining components and summarizes major progress in decoding physiological traits such as nutrient use efficiency and photosynthetic efficiency. It also discusses the integration of current knowledge about yield formation and crop improvement strategies including genome editing with conventional and molecular breeding.

Arachis Gene Pools and Genetic Improvement in Groundnut

Abstract: Groundnut (Arachis hypogaea L.) is an important oilseed and food crop in the world. The crop is predominantly grown in low input production systems in developing countries in Asia and Africa. There are several production constraints, both biotic and abiotic, to groundnut. Some of these are global in nature and the others are either regional or local. Four Arachis gene pools contain 80 species, distributed among nine sections are native to five countries of South America. Section Arachis contains tetraploid cultivated groundnut, divided into two subspecies and six botanical varieties and a number of cross-compatible diploid species with rich genetic diversity. International efforts have made significant progress in collection and conservation of these genetic resources, facilitating genetic improvement. Groundnut is an autogamous crop. The pedigree and bulk selection methods are more commonly used by the groundnut breeders. Conventional breeding, including cytogenetic manipulations introgressing genes from cross-compatible wild diploid species has been effective in some areas, while in others it has been tardy due to lack of proper and effective phenotyping tools and limited understanding of the genomics, genetics/inheritance, and underlying mechanisms influencing targeted traits. A greater diversification of parental resources (both cultivated and wild Arachis species) in breeding programs is required to develop new cultivars with diversified genetic backgrounds, which will enable them to perform better under the changing climatic/adverse conditions. Molecular breeding is in infancy. Infrequent and low polymorphisms have restricted the progress in the development and application of genetic maps, except in cases where polymorphic chromosomal regions have been introgressed from diploid wild Arachis species into A. hypogaea. Both conventional and nonconventional crop improvement efforts in groundnut need to concentrate on bridging the yield gap between the potential yield and the realized yield by alleviating major production constraints particularly in rainfed environment.