Molecular breeding

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

SNP Genotyping with Target Amplicon Sequencing Using a Multiplexed Primer Panel and Its Application to Genomic Prediction in Japanese Cedar, Cryptomeria japonica (L.f.) D.Don

Abstract: Along with progress in sequencing technology and accumulating knowledge of genome and gene sequences, molecular breeding techniques have been developed for predicting the genetic potential of individual genotypes and for selecting superior individuals. For Japanese cedar (Cryptomeria japonica (L.f.) D.Don), which is the most common coniferous species in Japanese forestry, we constructed a custom primer panel for target amplicon sequencing in order to simultaneously determine 3034 informative single nucleotide polymorphisms (SNPs). We performed primary evaluation of the custom primer panel with actual sequencing and in silico PCR. Genotyped SNPs had a distribution over almost the entire region of the C. japonica linkage map and verified the high reproducibility of genotype calls compared to SNPs obtained by genotyping arrays. Genotyping was performed for 576 individuals of the F1 population, and genomic prediction models were constructed for growth and wood property-related traits using the genotypes. Amplicon sequencing with the custom primer panel enables efficient obtaining genotype data in order to perform genomic prediction, manage clones, and advance forest tree breeding.

Assessing the Genetic Diversity of Chrysanthemum Cultivars with Microsatellites

Abstract: The morphological characteristics of chrysanthemum (Chrysanthemum ·morifolium) are rich in variation. However, as a result of the aneuploid polyploidy of the chrysanthemum genome and the lack of proper tools, the genomic information of this crop is limited. Development of microsatellite markers has been an increasing trend in crop genetic studies because of the applicability of these markers in breeding programs. In this study, we reported the development of a simple sequence repeat in chrysanthemums using a magnetic beads enrichment method. An enriched genomic library with AC and GT microsatellite motifs was constructed, and 53 positive clones were detected by a colony polymerase chain reaction (PCR) technique. Of these clones, 35 showed high-quality sequences, and 35 primer pairs were designed accordingly. Twenty-six (74.29%) of the 35 primer pairs revealed polymorphisms on a set of 40 chrysanthemum cultivars. There were 172 alleles amplified over 26 loci with an average of 6.615 alleles per locus. The mean values of gene diversity corrected for the sample size and the inbreeding coefficient were 0.609 and 0.119 over 26 loci, respectively, which indicated that the majority of the microsatellite loci is highly informative. Cluster analysis based on 26 polymorphic loci demonstrated that the selected cultivars were clustered according to geographical origin. This study shows the isolation efficiency of the magnetic beads technique; the abundance of microsatellites in chrysanthemum; and the potential application for the cultivar classification, the studies on genetic diversity, and molecular breeding of chrysanthemums, which is beneficial to promoting the conservation and sustainable use of this crop.

Breeding for Stem Borer and Gall Midge Resistance in Rice

Abstract: Breeding for insect-resistant varieties has been central to the integrated pest management as it offers a viable and ecologically acceptable approach. Status of progress made in breeding and adoption of resistant varieties against stem borers versus gall midge presents two contrasting scenarios. The conventional resistance breeding for yellow stem borer has not gained much impetus due to the lack of resistance sources in cultivated rice (Oryza sativa and O. glaberrima) gene pool, want of efficient insect rearing and varietal screening protocols, and inherently complex genetics of resistance. Hence, alternative approaches like wide hybridization to introgress resistance from other species of Oryza, transgenic approach to deploy Bt cry and other insecticidal genes and RNAi approach are being actively pursued. In contrast, high level of gall midge resistance is available in the crossable gene pool, insect rearing and greenhouse screening methods are well developed, genetics of resistance are well studied, molecular markers linked to R genes are developed, and many resistant rice varieties have been released for commercial cultivation and well adopted by farmers. To date 7 gall midge biotypes and 11 plant resistance genes have been reported. Nonetheless, the diversity in insect pest populations and continuous selection of virulent biotypes necessitate supplementation of conventional breeding techniques with molecular and transgenic approaches. Recent advances in the molecular breeding techniques and transgenic rice biotechnology present a great scope for enhanced varietal tolerance to biotic stresses. Status and prospects in this field are presented in this chapter.

Assisted Breeding in Sugar Beets

Abstract: Molecular insight and methods applied to plant breeding and germplasm enhancement is the goal of assisted breeding, also known as marker assisted breeding, marker assisted selection, molecular plant breeding, or genome-wide selection, among others. The basic idea is that most, if not all, heritable components of agronomic performance can be assayed with an unbiased, uniform, and comparatively inexpensive set of measures that are highly or completely correlated with phenotypic values. Typically such heritable components are genetically controlled, thus the panoply of DNA-based correlative methods should provide the requisite tools for assisted breeding to be successful. Whether DNA-based methods are successful in predicting agronomic performance depends on a host of considerations, many of which remain to be completely addressed for sugar beet, and thus assisted breeding remains somewhat empirical in practice, at least with respect to the specific traits of interest. Most sugar beet breeding and improvement programs have initiated assisted breeding efforts, primarily as a first step to discover marker associations with traits. These initial activities serve a number of important functions such as determining the complexity of trait inheritance, narrowing the possible range of genes and loci involved in phenotypic expression in different populations, and following the progress of sugar beet improvement following hybridization with wild and unadapted germplasm. It is unlikely that breeding will or should ever rely completely on assisted methods, however selection of the most promising germplasm can be greatly accelerated using molecular insights and knowledge.

Recent Progress in Rice Varietal Development for Abiotic Stress Tolerance

Abstract: Rapid climate change has aggravated the incidence of abiotic stresses, mainly; drought, salinity, submergence/flood, and temperature stress across the globe. Hence, sustaining crop productivity and quality under such a scenario has become as important as developing high-yielding varieties across all crop breeding programs. Rice is one of the major food crops ensuring global food security, but is highly sensitive to drought stress followed by salinity, high temperature (heat), and submergence/flood stress. Aided by the availability of high-quality reference genome, knowledge explosion in genomics, cost-effective high-throughput genotyping platforms and identification of major genes and genomic regions for the major abiotic stresses, rice breeders have shifted their focus from enhancing yield to developing climate smart varieties. Reconstitution of elite varieties by introgressing one or more genes and quantitative trait loci (QTLs) imparting abiotic stress tolerance through trait-linked or functional markers is the most common way of varietal development in rice. This can be considered as a landmark achievement since rice is the first crop wherein precision breeding has been employed at a large scale for abiotic stress tolerance though the molecular mechanism of tolerance still remains unknown except for Sub1A and SKC1. This chapter provides details on recent developments in rice breeding programs around the globe for enhanced abiotic stress tolerance. The list of major QTLs identified is provided for heat tolerance where molecular breeding at a large scale is yet to see the light of the day. Marker assisted backcross breeding and marker assisted recurrent selection for transfer or pyramiding of identified QTL/genes to elite varieties are introduced briefly.