Molecular breeding

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

Development of novel microRNA-based genetic markers in foxtail millet for genotyping applications in related grass species

Abstract: DNA markers are important in molecular breeding, and, hence, considering its prominence, a variety of DNA-based molecular markers have been explored and developed for expediting crop improvement programs. microRNA (miRNA)-based molecular marker is a type of functional markers exploited predominantly in animal sciences, but reported in very few plants. Considering the efficacy, stability and transferability potential of the miRNA-based markers, the present study was conducted to develop these markers in the model crop foxtail millet. The pre-miRNA sequences of foxtail millet and other related grasses including rice, maize, wheat, sorghum and Brachypodium were retrieved and aligned for identifying the conserved regions. One hundred and seventy-six primer pairs were designed for these consensus sequences, and all these 176 miRNA-based markers were mapped onto foxtail millet genome. Of the 176 markers, 66 were chosen for further experimentations based on representing the nine chromosomes of foxtail millet and presence of highly conserved regions. All the 66 markers showed 100 % amplification in five cultivars of foxtail millet. Moreover, all the markers showed a higher level of cross-genera transferability potential with an average of ~67 % in millets and non-millet species. This is the first report on the development of novel miRNA-based markers in foxtail millet. Promisingly, these markers would serve as novel genotyping tool for various molecular breeding approaches aiming at crop improvement in millets and non-millet species.

Development of multiple SNP marker panels affordable to breeders through genotyping by target sequencing (GBTS) in maize

Abstract: The development of a high-throughput genotyping platform with high quality, flexibility, and affordable genotyping cost is critical for marker-assisted breeding. In this study, a genotyping by target sequencing (GBTS) platform was developed in maize, which can be realized for a small number of markers (several to 5 K) through multiplex PCR (GenoPlexs) and for a large number of markers (1 to 45 K) through in-solution capture. The later was used for development of four SNP marker panels (GenoBaits Maize) containing 20 K, 10 K, 5 K, and 1 K markers. Two genotype panels, one consisting 96 representative worldwide maize inbred lines and the other containing 387 breeding lines developed in our maize breeding programs, were used to test and validate the developed marker panels. First, a 20 K SNP panel, with markers evenly distributed across maize genome, was developed from a 55 K SNP array with improved genome coverage. From this single marker panel, 20 K, 10 K, 5 K, and 1 K SNP markers can be generated by sequencing the samples at the average sequencing depths of 50×, 20×, 7.5×, and 2.5×, respectively. Highly consistent marker genotypes were obtained between the four marker panels and the 55 K array (over 95%) and between two biological replications (over 98%). Also, highly consistent phylogenetic relationships were generated by using four marker panels and two genotype panels, providing strong evidence for the reliability of SNP markers and GBTS genotyping platform. Cost-benefit analysis indicated that the genotypic selection cost based on the GBTS in maize was lower than phenotypic selection, allowing GBTS an affordable genotyping platform for marker-assisted breeding. Integration of this affordable genotyping platform with other breeding platforms and open-source breeding network would greatly facilitate the molecular breeding activities in small- and medium-size companies and developing countries. The four marker panels could be used for many fields of marker application, including germplasm evaluation, genetic mapping, marker-assisted selection (including genomic selection), and plant variety protection.

An SNP-based saturated genetic map and QTL analysis of fruit-related traits in Zucchini using Genotyping-by-sequencing

Abstract: Cucurbita pepo is a cucurbit with growing economic importance worldwide. Zucchini morphotype is the most important within this highly variable species. Recently, transcriptome and Simple Sequence Repeat (SSR)- and Single Nucleotide Polymorphism (SNP)-based medium density maps have been reported, however further genomic tools are needed for efficient molecular breeding in the species. Our objective is to combine currently available complete transcriptomes and the Zucchini genome sequence with high throughput genotyping methods, mapping population development and extensive phenotyping to facilitate the advance of genomic research in this species. We report the Genotyping-by-sequencing analysis of a RIL population developed from the inter subspecific cross Zucchini x Scallop (ssp. pepo x ssp. ovifera). Several thousands of SNP markers were identified and genotyped, followed by the construction of a high-density linkage map based on 7,718 SNPs (average of 386 markers/linkage group) covering 2,817.6 cM of the whole genome, which is a great improvement with respect to previous maps. A QTL analysis was performed using phenotypic data obtained from the RIL population from three environments. In total, 48 consistent QTLs for vine, flowering and fruit quality traits were detected on the basis of a multiple-environment analysis, distributed in 33 independent positions in 15 LGs, and each QTL explained 1.5–62.9% of the phenotypic variance. Eight major QTLs, which could explain greater than 20% of the phenotypic variation were detected and the underlying candidate genes identified. Here we report the first SNP saturated map in the species, anchored to the physical map. Additionally, several consistent QTLs related to early flowering, fruit shape and length, and rind and flesh color are reported as well as candidate genes for them. This information will enhance molecular breeding in C. pepo and will assist the gene cloning underlying the studied QTLs, helping to reveal the genetic basis of the studied processes in squash.

Integrating genomics for chickpea improvement: Achievements and opportunities

Abstract: Integration of genomic technologies with breeding efforts have been used in recent years for chickpea improvement. Modern breeding along with low cost genotyping platforms have potential to further accelerate chickpea improvement efforts. The implementation of novel breeding technologies is expected to contribute substantial improvements in crop productivity. While conventional breeding methods have led to development of more than 200 improved chickpea varieties in the past, still there is ample scope to increase productivity. It is predicted that integration of modern genomic resources with conventional breeding efforts will help in the delivery of climate-resilient chickpea varieties in comparatively less time. Recent advances in genomics tools and technologies have facilitated the generation of large-scale sequencing and genotyping data sets in chickpea. Combined analysis of high-resolution phenotypic and genetic data is paving the way for identifying genes and biological pathways associated with breeding-related traits. Genomics technologies have been used to develop diagnostic markers for use in marker-assisted backcrossing programmes, which have yielded several molecular breeding products in chickpea. We anticipate that a sequence-based holistic breeding approach, including the integration of functional omics, parental selection, forward breeding and genome-wide selection, will bring a paradigm shift in development of superior chickpea varieties. There is a need to integrate the knowledge generated by modern genomics technologies with molecular breeding efforts to bridge the genome-to-phenome gap. Here, we review recent advances that have led to new possibilities for developing and screening breeding populations, and provide strategies for enhancing the selection efficiency and accelerating the rate of genetic gain in chickpea.