STMS markers related to Ascochyta blight resistance in chickpea

Chickpea (Cicer arietinum L.) is one of the important legume crops and is cultivated in large-scale throughout Türkiye as well as the world. Ascochyta blight, caused by the fungal phytopathogen Ascochyta rabiei, is the leading reason for the highest yield losses among the diseases known for chickpea. The pathogen exhibits high genetic diversity in Türkiye. Therefore, resistancy using Sequence Tagged Microsatellite Site (STMS) markers related with the genes that provide resistant against Ascochyta blight was investigated for the 205 chickpea breeding lines grown in different parts of Türkiye. The analysis for Ascochyta blight resistance was performed using Ta2, Ta146 and Ts54. It was demonstrated that Ta2, Ts54 and Ta146 were the STMS markers having distinguishable features for the detection of Ascochyta blight resistance and were shown to be used in credible fashion for the selection of resistant chickpea breeding lines.

Achievements of agricultural biotechnology: An initiative to double the farmer’s income through cutting edge technology

The population of the world is increasing nearly exponentially over time. To feed this population following the environment conservation protocol, it is essential to enhance the agricultural productivity even in the synchronizing agrarian land use pattern. To enhance the quality and productivity in agriculture sector, introducing the cutting edge technology is need of the hour.From ancient times, traditional approaches like selective breeding, adoption of agronomic management practices and application of indigenous technical knowledge have been used to attain resilience against various abiotic and biotic stresses. However, these traditional approaches are not sufficient to tackle the increasing repercussions of climate change and feed quality food to the expanding population. Therefore, in order to address these issues of climate change, population explosion and malnutrition, biotechnological interventions can be a promising approach. In the past, biotechnology based approaches have given successful products like Herbicide-resistant Soybean, Pusa Basmati 1, Bt Cotton, Bt Brinjal, Flavr-Savr tomato, a therapeutically significant product of Lithospermum erythrorhizon and Panax ginseng. Besides that many more need based products are in pipeline which is under scrutiny of regulatory bodies, policymakers and environmentalists. It is profoundly expected that in the coming day’s agricultural biotechnology applications will bring revolutionary changes to existing agricultural scenario. Therefore, in this review, we have summarized the achievement of agricultural biotechnology that is assisting to enhance the agricultural produce to double the income of farmers. However, this much is not enough; hence full utilization of all the sustainable agricultural biotechnological tools must come into the existence that definitely will boost the agricultural productivity.

Bovine TMEM95 gene: Polymorphisms detecting in five Chinese indigenous cattle breeds and their association with growth traits

BACKGROUND: Transmembrane protein 95 (TMEM95) plays a role in male fertility. Previous studies showed that genes with a significant impact on reproductive traits can also affect the growth traits of livestock. Thus, we speculated that the genetic variation of TMEM95 gene may have effects on growth traits of cattle. RESULTS: Two SNPs were genotyped. The rs136174626 and rs41904693 were in the intron 4 and 30 -untranslated region, respectively. The linkage disequilibrium analysis illustrated that these two loci were not linked. The rs136174626 was associated with six growth traits of Nanyang cattle, four traits of Luxi cattle, and three traits of Ji'an cattle. For rs41904693 locus, the GG individuals had greater body height and abdominal girth in Ji' an cattle than TT and TG individuals. In Jinnan cattle, GG and TT individuals had greater body height, height at hip cross, body length, and heart girth than TG individuals. The potential splice site prediction results suggest that the rs136174626 may influence the splicing efficiency of TMEM95, and the miRNA binding site prediction results showed that the rs41904693 may influence the expression of TMEM95 by affecting the binding efficiency of Bta-miR-1584 and TMEM95 30 -UTR. CONCLUSIONS: The findings of the study suggested that the two SNPs in TMEM95 could be a reliable basis for molecular breeding in cattle.

Development direction of molecular breeding of medicinal plants / 中国中药杂志

To breed new varieties of medicinal plants with high resistance is the premise to ensure the production of high-quality medicinal materials. Molecular breeding using modern molecular biology and genetic technology can save time and effort and realize rapid and accurate breeding. Here we are trying to summarize the difference of breeding characteristics between medicinal plants and crops such as genetic background and breeding purpose. The strategy of molecular breeding of medicinal plants was summarized, and the four-phases breeding based on high-throughput sequencing and target gene mining was emphasized. We put forward the current molecular breeding of medicinal plants in the condition of four phases breeding is the optimal technological way of breeding, and gene editing breeding is the direction of medicinal plants breeding.

Production of wheat-doubled haploids resistant to eyespot supported by marker-assisted selection

BACKGROUND: Wheat is one of the most important crops cultivated all over the world. New high-yielding cultivars that are more resistant to fungal diseases have been permanently developed. The present study aimed at the possibility of accelerating the process of breeding new cultivars, resistant to eyespot, by using doubled haploids (DH) system supported by marker-assisted selection. RESULTS: Two highly resistant breeding lines (KBP 0916 and KBH 4942/05) carrying Pch1 gene were crossed with the elite wheat genotypes. Hybrid plants of early generations were analyzed using endopeptidase EpD1 and two SSR markers linked to the Pch1 locus. Selected homozygous and heterozygous genotypes for the Pch1-linked EpD1b allele were used to produce haploid plants. Molecular analyses were performed on haploids to identify plants possessing Pch1 gene. Chromosome doubling was performed only on haploid plants with Pch1 gene. Finally, 65 DH lines carrying eyespot resistance gene Pch1 and 30 lines without this gene were chosen for the eyespot resistance phenotyping in a field experiment. CONCLUSIONS: Results of the experiment confirmed higher resistance to eyespot of the genotypes with Pch1 in comparison to those without this gene. This indicates the efficiency of selection at the haploid level.

Molecular genetics research of medicinal plants / 中国中药杂志

With the development of various biotechnology,the research on molecular genetics of medicinal plants has gradually deepened. In this paper,the research system of molecular genetics of medicinal plants was proposed for the first time,which was elaborated from the aspects of genetic resources,genome,gene function and research methods. The application fields of medicinal plant mainly contain species identification,molecular breeding and biosynthesis. The research directions of molecular genetics of medicinal plants in genetic resources,model platform,synthetic biology and molecular breeding were put forward,which include 1 000 genome projects of medicinal plants,model species and mutant libraries,gene original libraries of heterologous synthetic systems,construction gene original library and specific chassis cells in heterologous synthesis system of active ingredient,breeding of new varieties of medicinal plants with high active ingredient and high resistance based on molecular markers andtransgenes.

Statues and research strategy of molecular breeding in Artemisia annua / 中国中药杂志

Malaria is one of the three most deadly diseases in the world. Artemisinin is the first line and effective drug for treating malaria, and only can be extracted from Artemisia annua. Therefore, it is of great significance to cultivate new varieties of A. annua with high artemisinin content. Based on the germplasm bank and the whole genome, transcriptome and genetic map, the authors can explore high-quality genes, stress-resistant genes and genetic markers which have been used for rapid breeding of superior varieties of A. annua. So these methods of molecular breeding will become the main breeding direction of A. annua in the future. The breeding times of new varieties of A. annua can be shortened with molecular breeding technology. Based on the genetic background and the current situation of molecular breeding of A. annua, the strategy and technical route of molecular breeding were discussed and worked out in this paper, which provided a guidance and scientific reference for molecular breeding of A. annua in the future.

Development and application of KASP marker for high throughput detection of AhFAD2 mutation in peanut

Background: Cultivated peanut (Arachis hypogaea L.) is a major oilseed crop worldwide. Fatty acid composition of peanut oil may affect the flavor and shelf life of the resulting food products. Oleic acid and linoleic acid are the major fatty acids of peanut oil. The conversion from oleic acid to linoleic acid is controlled by theΔ12 fatty acid desaturase (FAD) encoded byAhFAD2AandAhFAD2B, two homoeologous genes from A and B subgenomes, respectively. One nucleotide substitution (G:C→A:T) ofAhFAD2Aand an "A" insertion ofAhFAD2Bresulted in high-oleic acid phenotype. Detection ofAhFAD2mutation had been achieved by cleaved amplified polymorphic sequence (CAPS), real-time polymerase chain reaction (qRT-PCR) and allele-specific PCR (AS-PCR). However, a low cost, high throughput and high specific method is still required to detectAhFAD2genotype of large number of seeds. Kompetitive allele specific PCR (KASP) can detect both alleles in a single reaction. The aim of this work is to develop KASP for detectionAhFAD2genotype of large number of breeding materials. Results: Here, we developed a KASP method to detect the genotypes of progenies between high oleic acid peanut and common peanut. Validation was carried out by CAPS analysis. The results from KASP assay and CAPS analysis were consistent. The genotype of 18 out of 179 BC4F2seeds was aabb. Conclusions: Due to high accuracy, time saving, high throughput feature and low cost, KASP is more suitable fordeterminingAhFAD2genotype than other methods.

Strategies of elucidation of biosynthetic pathways of natural products / 中国中药杂志

Elucidation of the biosynthetic pathways of natural products is not only the major goal of herb genomics, but also the solid foundation of synthetic biology of natural products. Here, this paper reviewed recent advance in this field and put forward strategies to elucidate the biosynthetic pathway of natural products. Firstly, a proposed biosynthetic pathway should be set up based on well-known knowledge about chemical reactions and information on the identified compounds, as well as studies with isotope tracer. Secondly, candidate genes possibly involved in the biosynthetic pathway were screened out by co-expression analysis and/or gene cluster mining. Lastly, all the candidate genes were heterologously expressed in the host and then the enzyme involved in the biosynthetic pathway was characterized by activity assay. Sometimes, the function of the enzyme in the original plant could be further studied by RNAi or VIGS technology. Understanding the biosynthetic pathways of natural products will contribute to supply of new leading compounds by synthetic biology and provide "functional marker" for herbal molecular breeding, thus but boosting the development of traditional Chinese medicine agriculture.

Integrated genomics and molecular breeding approaches for dissecting the complex quantitative traits in crop plants.

The enormous population growth, climate change and global warming are now considered major threats to agriculture and world’s food security. To improve the productivity and sustainability of agriculture, the development of highyielding and durable abiotic and biotic stress-tolerant cultivars and/climate resilient crops is essential. Henceforth, understanding the molecular mechanism and dissection of complex quantitative yield and stress tolerance traits is the prime objective in current agricultural biotechnology research. In recent years, tremendous progress has been made in plant genomics and molecular breeding research pertaining to conventional and next-generation whole genome, transcriptome and epigenome sequencing efforts, generation of huge genomic, transcriptomic and epigenomic resources and development of modern genomics-assisted breeding approaches in diverse crop genotypes with contrasting yield and abiotic stress tolerance traits. Unfortunately, the detailed molecular mechanism and gene regulatory networks controlling such complex quantitative traits is not yet well understood in crop plants. Therefore, we propose an integrated strategies involving available enormous and diverse traditional and modern –omics (structural, functional, comparative and epigenomics) approaches/resources and genomics-assisted breeding methods which agricultural biotechnologist can adopt/utilize to dissect and decode the molecular and gene regulatory networks involved in the complex quantitative yield and stress tolerance traits in crop plants. This would provide clues and much needed inputs for rapid selection of novel functionally relevant molecular tags regulating such complex traits to expedite traditional and modern marker-assisted genetic enhancement studies in target crop species for developing high-yielding stress-tolerant varieties.

ANÁLISIS DE ESTs DE YUCA (Manihot esculenta): UNA HERRAMIENTA PARA EL DESCUBRIMIENTO DE GENES / Analysis of Cassava (Manihot esculenta) ESTs: A Tool for the Discovery of Genes

La yuca (Manihot esculenta) constituye la base de la alimentación para más de 1.000 millones de personas en el mundo, consolidándose como el cuarto cultivo más importante en el mundo después del arroz, el maíz y el trigo. La yuca es considerada como un cultivo relativamente tolerante a condiciones de estrés abiótico y biótico; sin embargo estas características se encuentran principalmente en variedades no comerciales. Las estrategias de mejoramiento genético convencional o mediadas por transformación genética representan una alternativa para introducir las características deseadas dentro de las variedades comerciales. Un paso fundamental con miras a acelerar los procesos de mejoramiento genético en yuca requiere el descubrimiento de los respectivos genes relacionados con las características buscadas, para lo cual los ESTs (del inglés Expressed Sequence Tags) son una vía rápida para este fin. En este estudio se realizó un análisis de la colección completa de ESTs disponibles en yuca, representada por 80.459 secuencias, los cuales fueron ensamblados en un conjunto de 29.231 genes únicos (unigen), representado por 10.945 contigs y 18.286 singletones. Estos 29.231 genes únicos pueden representar cerca del 80% de los genes del genoma de yuca. Entre el 5 y 10% de los unigenes de yuca no presentaron similitud con las secuencias presentes en las bases de datos de NCBI y pueden constituir genes específicos de yuca. A un grupo de secuencias del set unigen (29%) fue posible asignarles una categoría funcional de acuerdo al vocabulario Gene Ontology. El componente función molecular es el mejor representado con 43% de las secuencias, seguido por el componente proceso biológico (38%) y finalmente el componente celular (19%). Dentro de la colección de ESTs de yuca se identificaron 3.709 microsatélites que podrán ser empleados como marcadores moleculares. Este estudio representa una contribución importante al conocimiento de la estructura genómica funcional de la yuca y se constituye en una herramienta para la identificación de genes asociados a características de interés agrícola para posteriores programas de mejoramiento genético.

Cassava (Manihot esculenta) is the main source of calories for more than 1,000 millions of people around the world and has been consolidated as the fourth most important crop after rice, corn and wheat. Cassava is considered tolerant to abiotic and biotic stress conditions; nevertheless these characteristics are mainly present in non-commercial varieties. Genetic breeding strategies represent an alternative to introduce the desirable characteristics into commercial varieties. A fundamental step for accelerating the genetic breeding process in cassava requires the identification of genes associated to these characteristics. One rapid strategy for the identification of genes is the possibility to have a large collection of ESTs (Expressed Sequence Tag). In this study, a complete analysis of cassava ESTs was done. The cassava ESTs represent 80,459 sequences which were assembled in a set of 29,231 unique genes (unigen), comprising 10,945 contigs and 18,286 singletones. These 29,231 unique genes represent about 80% of the genes of the cassava’s genome. Between 5% and 10% of the unigenes of cassava not show similarity to any sequences present in the NCBI database and could be consider as cassava specific genes. A functional category was assigned to a group of sequences of the unigen set (29%) following the Gene Ontology vocabulary. The molecular function component was the best represented with 43% of the sequences, followed by the biological process component (38%) and finally the cellular component with 19%. In the cassava ESTs collection, 3,709 microsatellites were identified and they could be use as molecular markers. This study represents an important contribution to the knowledge of the functional genomic structure of cassava and constitutes an important tool for the identification of genes associated to agricultural characteristics of interest that could be employed in cassava breeding programs.

The genetic dissection of quantitative traits in crops

Most traits of interest in plant breeding show quantitative inheritance, which complicate the breeding process since phenotypic performances only partially reflects the genetic values of individuals. The genetic variation of a quantitative trait is assumed to be controlled by the collective effects of quantitative trait loci (QTLs), epistasis (interaction between QTLs), the environment, and interaction between QTL and environment. Exploiting molecular markers in breeding involve finding a subset of markers associated with one or more QTLs that regulate the expression of complex traits. Many QTL mapping studies conducted in the last two decades identified QTLs that generally explained a significant proportion of the phenotypic variance, and therefore, gave rise to an optimistic assessment of the prospects of markers assisted selection. Linkage analysis and association mapping are the two most commonly used methods for QTL mapping. This review provides an overview of the two QTL mapping methods, including mapping population type and size, phenotypic evaluation of the population, molecular profiling of either the entire or a subset of the population, marker-trait association analysis using different statistical methods and software as well as the future prospects of using markers in crop improvement.