Molecular Breeding Technologies Research Articles

Advances in Mechanism and Application of Molecular Breeding of Medicinal Mushrooms: A Review.

With the development of molecular biology and genomics technology, mushroom breeding methods have changed from single traditional breeding to molecular breeding. Compared with traditional breeding methods, molecular breeding has the advantages of short time and high efficiency. It breaks through the restrictive factors of conventional breeding and improves the accuracy of breeding. Molecular breeding technology is gradually applied to mushroom breeding. This paper summarizes the concept of molecular breeding and the application progress of various molecular breeding technologies in mushroom breeding, in order to provide reference for future research on mushroom breeding.

Loss-of-function of triacylglycerol lipases are associated with low flour rancidity in pearl millet [Pennisetum glaucum (L.) R. Br.

Pearl millet is an important cereal crop of semi-arid regions since it is highly nutritious and climate resilient. However, pearl millet is underutilized commercially due to the rapid onset of hydrolytic rancidity of seed lipids post-milling. We investigated the underlying biochemical and molecular mechanisms of rancidity development in the flour from contrasting inbred lines under accelerated aging conditions. The breakdown of storage lipids (triacylglycerols; TAG) was accompanied by free fatty acid accumulation over the time course for all lines. The high rancidity lines had the highest amount of FFA by day 21, suggesting that TAG lipases may be the cause of rancidity. Additionally, the high rancidity lines manifested substantial amounts of volatile aldehyde compounds, which are characteristic products of lipid oxidation. Lipases with expression in seed post-milling were sequenced from low and high rancidity lines. Polymorphisms were identified in two TAG lipase genes (PgTAGLip1 and PgTAGLip2) from the low rancidity line. Expression in a yeast model system confirmed these mutants were non-functional. We provide a direct mechanism to alleviate rancidity in pearl millet flour by identifying mutations in key TAG lipase genes that are associated with low rancidity. These genetic variations can be exploited through molecular breeding or precision genome technologies to develop elite pearl millet cultivars with improved flour shelf life.

Identification of stress-related genes by co-expression network analysis based on the improved turbot genome

Turbot (Scophthalmus maximus), commercially important flatfish species, is widely cultivated in Europe and China. With the continuous expansion of the intensive breeding scale, turbot is exposed to various stresses, which greatly impedes the healthy development of turbot industry. Here, we present an improved high-quality chromosome-scale genome assembly of turbot using a combination of PacBio long-read and Illumina short-read sequencing technologies. The genome assembly spans 538.22 Mb comprising 27 contigs with a contig N50 size of 25.76 Mb. Annotation of the genome assembly identified 104.45 Mb repetitive sequences, 22,442 protein-coding genes and 3,345 ncRNAs. Moreover, a total of 345 stress responsive candidate genes were identified by gene co-expression network analysis based on 14 published stress-related RNA-seq datasets consisting of 165 samples. Significantly improved genome assembly and stress-related candidate gene pool will provide valuable resources for further research on turbot functional genome and stress response mechanism, as well as theoretical support for the development of molecular breeding technology for resistant turbot varieties.

Climate-Resilient Crops: Breeding Strategies for Extreme Weather Conditions

Climate change poses a significant threat to global agriculture, impacting crop productivity and food security. The increased frequency and severity of extreme weather events, such as droughts, floods, heatwaves, and cold spells, necessitate the development of climate-resilient crops. Through innovative breeding strategies, we can adapt our agricultural systems to these changing conditions. This review explores the latest advancements in crop breeding techniques, including traditional breeding methods, molecular breeding, and gene editing technologies like CRISPR/Cas9. We discuss the integration of phenotyping and genotyping, the role of genetic diversity, and the importance of breeding for multiple stress resistances. Additionally, we highlight successful case studies and propose future directions for research and policy to support the development and widespread adoption of climate-resilient crops. This comprehensive overview aims to provide insights into the current state of crop breeding and to identify key areas for future innovation and collaboration in the quest to secure global food systems against the impacts of climate change

Overexpression of adenosine 5′-monophosphate deaminase increased umami substance—Inosine 5′- mononucleotide and promoted Neopyropia yezoensis quality

Precision molecular breeding technology plays an important role in improving the yield and quality of cultivated marine crops. In this study, we aimed to improve the quality of Neopyropia yezoensis, one of the important economic seaweeds. We constructed overexpression (OE)-, co-suppression (Ci)-, and RNAi (Ri)-type mutants of Nyampd (AMP deaminase of N. yezoensis), which could catalyze the decomposition of AMP into the umami substance inosine 5′- mononucleotide (IMP) through the genetic transformation system of N. yezoensis. Our results showed that the IMP content and growth rate of OE strain were significantly higher than those of wild type. In addition, in knockdown strains (Ci/Ri), a phenomenon similar to genetic compensation in knockout research occurred, i.e., the expression of Nyampd2 (isozyme of Nyampd) was significantly upregulated in Ri/Ci strains, and the IMP content increased in Ci/Ri strains. These results provide important knowledge for precise molecular breeding and genetic transformation research of N. yezoensis.

Genomic prediction of cotton fibre quality and yield traits using Bayesian regression methods

Genomic selection or genomic prediction (GP) has increasingly become an important molecular breeding technology for crop improvement. GP aims to utilise genome-wide marker data to predict genomic breeding value for traits of economic importance. Though GP studies have been widely conducted in various crop species such as wheat and maize, its application in cotton, an essential renewable textile fibre crop, is still significantly underdeveloped. We aim to develop a new GP-based breeding system that can improve the efficiency of our cotton breeding program. This article presents a GP study on cotton fibre quality and yield traits using 1385 breeding lines from the Commonwealth Scientific and Industrial Research Organisation (CSIRO, Australia) cotton breeding program which were genotyped using a high-density SNP chip that generated 12,296 informative SNPs. The aim of this study was twofold: (1) to identify the models and data sources (i.e. genomic and pedigree) that produce the highest prediction accuracies; and (2) to assess the effectiveness of GP as a selection tool in the CSIRO cotton breeding program. The prediction analyses were conducted under various scenarios using different Bayesian predictive models. Results highlighted that the model combining genomic and pedigree information resulted in the best cross validated prediction accuracies: 0.76 for fibre length, 0.65 for fibre strength, and 0.64 for lint yield. Overall, this work represents the largest scale genomic selection studies based on cotton breeding trial data. Prediction accuracies reported in our study indicate the potential of GP as a breeding tool for cotton. The study highlighted the importance of incorporating pedigree and environmental factors in GP models to optimise the prediction performance.

The Next Generation of Rice: Inter-Subspecific Indica-Japonica Hybrid Rice.

Rice (Oryza sativa) is an important food crop and has two subspecies, indica and japonica. Since the last century, four generations of rice varieties have been applied to rice production. Semi-dwarf rice, intra-subspecific hybrid rice, and inter-subspecific introgression rice were developed successively by genetic modification based on the first generation of tall rice. Each generation of rice has greater yield potential than the previous generation. Due to the stronger heterosis of indica-japonica hybrids, utilization of the inter-subspecific heterosis has long been of interest. However, indica-japonica hybrid sterility hinders the utilization of heterosis. In the past decades, indica-japonica hybrid sterility has been well understood. It is found that indica-japonica hybrid sterility is mainly controlled by six loci, S5, Sa, Sb, Sc, Sd, and Se. The indica-japonica hybrid sterility can be overcome by developing indica-compatible japonica lines (ICJLs) or wide-compatible indica lines (WCILs) using genes at the loci. With the understanding of the genetic and molecular basis of indica-japonica hybrid sterility and the development of molecular breeding technology, the development of indica-japonica hybrid rice has become possible. Recently, great progress has been made in breeding indica-japonica hybrid rice. Therefore, the indica-japonica hybrid rice will be the next generation of rice. It is expected that the indica-japonica hybrid rice will be widely applied in rice production in the near future.

Feature Compression Applications of Genetic Algorithm.

With the rapid development of molecular breeding technology and many new varieties breeding, a method is urgently needed to identify different varieties accurately and quickly. Using this method can not only help farmers feel convenient and efficient in the normal cultivation and breeding process but also protect the interests of breeders, producers and users. In this study, single nucleotide polymorphism (SNP) data of 533 Oryza sativa, 284 Solanum tuberosum and 247 Sus scrofa and 544 Manihot esculenta Crantz were used. The original SNPs were filtered and screened to remove the SNPs with deletion number more than 1% or the homozygous genotype 0/0 and 1/1 number less than 2. The correlation between SNPs were calculated, and the two adjacent SNPs with correlation R2 > 0.95 were retained. The genetic algorithm program was developed to convert the genotype format and randomly combine SNPs to calculate a set of a small number of SNPs which could distinguish all varieties in different species as fingerprint data, using Matlab platform. The successful construction of three sets of fingerprints showed that the method developed in this study was effective in animals and plants. The population structure analysis showed that the genetic algorithm could effectively obtain the core SNPs for constructing fingerprints, and the fingerprint was practical and effective. At present, the two-dimensional code of Manihot esculenta Crantz fingerprint obtained by this method has been applied to field planting. This study provides a novel idea for the Oryza sativa, Solanum tuberosum, Sus scrofa and Manihot esculenta Crantz identification of various species, lays foundation for the cultivation and identification of new varieties, and provides theoretical significance for many other species fingerprints construction.

Genomic structure of Bali cattle based on linkage disequilibrium and effective population size analyses using 50K single nucleotide polymorphisms data

Background and aim:Bali Cattle (Bos j. javanicus) is a local breed originating in Indonesia, accounting for 32.3% of the total cattle population. To date, no studies of the genetic structure and demographic status of Bali cattle have been conducted, even though the breeding of Bali cattle has a long and unique history that is likely to have impacted its genetic diversity. Therefore, a study that used molecular breeding technologies to characterize the demography of Bali cattle would be timely. This study aimed to examine genome diversity in Bali cattle and estimate the linkage disequilibrium (LD) and effective population size (Ne) values in the cattle population.Materials and Methods:In this study, we explored the population structure and genetic diversity of Bali cattle using genomic-level analyses. Our study primarily studied cattle that had been bred in livestock breeding centers since these breeds had subsequently spread throughout Indonesia. We focused on characterizing the genetic structure, determining the level of LD present, and estimating the Ne of the Bali cattle population. The genomic data used for this study were obtained from DNA samples of 48 Bali cattle collected at the Breeding Center of Bali Cattle as well as 54 genomic samples from Bali cattle collected elsewhere in Indonesia that had been used in recent publications. This genomic dataset included exclusively 50K single nucleotide polymorphisms (SNP) array (Illumina Bovine 50SNP bead chip, Illumina, USA) data.Results:We found that the LD values of Bali cattle from the breeding center and those raised elsewhere were 0.48±0.43 and 0.39±0.40, respectively. Subsequently, the Ne value of Bali cattle from the breeding center and farmers was 151 and 96, respectively.Conclusion:Our results suggest that the selection program of the breeding center is beneficial for maintaining the genetic diversity of Bali cattle.

Haze in Beer: Its Formation and Alleviating Strategies, from a Protein-Polyphenol Complex Angle.

Beer is one of the oldest and most widely consumed alcoholic beverages. Haze formation in beer is a serious quality problem, as it largely shortens the shelf life and flavor of beer. This paper reviews the factors affecting haze formation and strategies for reducing haze. Haze formation is mainly associated with specific chemical components in malt barley grains, such as proteins. The main factor causing haze formation is a cross-linking of haze active (HA) proteins and HA polyphenols. Many HA proteins and their editing genes or loci have been identified by proteomics and quantitative trait locus (QTL) analysis, respectively. Although some technical approaches have been available for reducing haze formation in beer, including silica and polyvinylpolypyrrolidone (PVPP) adsorbent treatments, the cost of beer production will increase and some flavor will be lost due to reduced relevant polyphenols and proteins. Therefore, breeding the malt barley cultivar with lower HA protein and/or HA polyphenols is the most efficient approach for controlling haze formation. Owing to the completion of barley whole genome sequencing and the rapid development of modern molecular breeding technology, several candidate genes controlling haze formation have been identified, providing a new solution for reducing beer haze.

Drought stress in sorghum: Mitigation strategies, breeding methods and technologies—A review

AbstractAgriculture accounts for 70% of the global use of available freshwater. Projections show that demand for water will increase significantly due to climate change, population growth and development of agricultural enterprises globally. There is a need to develop water‐use efficient crop cultivars for sustainable agricultural production. Sorghum [Sorghum bicolor (L.) Moench.] is a powerhouse crop in drier regions supporting more than 500 million people. It is a relatively drought‐tolerant crop adapted to grow and yield in marginal environments where other dominant crops such as maize and wheat fail to survive. However, the mean yield of sorghum in the semi‐arid regions has stagnated around 1.0 ton/ha compared with the global average of 2.5 ton/ha, mainly due to recurrent droughts and heat stress. Breeding for drought‐tolerant cultivars is an economic and sustainable mitigation strategy against the current and projected drought stress. Therefore, the objectives of this review were to document the impact of drought stress and the key mitigation strategies under drought‐prone semi‐arid sorghum production systems. The first section of the review highlighted the impact of drought and its mitigation strategies emphasizing on the use of drought‐tolerant cultivars as the best strategy. This is followed by perspectives on aspects of drought‐response mechanisms, breeding methods and complementary technologies for drought tolerance. Integration of the conventional and molecular breeding technologies with rapid generation advancement methods could reduce the breeding cycle and increase the efficiency of deploying new varieties. Information presented in this review will guide agronomists and breeders to develop and deploy drought‐tolerant sorghum cultivars that are adapted to the changing production environments in the semi‐arid regions.

Fertility regulation and molecular design hybrid breeding in crops

<p indent=0mm>Fertility regulation affects crop yield as well as heterosis utilization. Here we summarize the genetic basis and molecular regulatory mechanism of male sterility and hybrid sterility in crops. The advances include cytoplasmic male sterility and its application in three-line hybrid breeding, photoperiod- and temperature-sensitive genic male sterility and its application in two-line hybrid breeding, biotechnology-based male sterility system and its application by molecular design breeding technology, and hybrid fertility and its application in distant hybrid breeding. On this basis, we discuss the bottleneck and strategies for exploring mechanisms of crop fertility regulation and molecular design hybrid breeding in China, with future trend predicted.

Discovery of a naturally-occurring allele of eIF4E1.S in Nicotiana tabacum and development of a co-dominant marker

Potato virus Y (PVY) is one of the most problematic pathogens affecting tobacco production. Genetic resistance to PVY in cultivated tobacco is mediated by recessive mutations, including the locus designated VAM, and its derived mutant va, both of which were previously shown to contain large chromosomal deletions. Among the genes deleted in lines containing VAM or va is eIF4E1.S, a gene whose protein product has been shown to facilitate infection by certain potyviruses, including PVY. Because the extent of the deletions and the exact nature of their specific breakpoints have not been precisely established for VAM or va, it has not been possible to develop co-dominant markers to facilitate their transfer to elite varieties using molecular breeding technologies. Here, we report the discovery of a novel naturally-occurring allele of eIF4E1.S from the Chinese tobacco landrace Fuquanliuye, designated eIF4E1.Fu, which lacks a genomic region of approximately 27 kb, including the 3'-end of eIF4E1.S. Characterization of the deletion junction enabled the development of a co-dominant PCR-based marker specific for eIF4E1.Fu, which can distinguish eIF4E1.S/eIF4E1.Fu heterozygotes from both homozygous classes. Using this co-dominant marker, we genotyped F2 plants segregating for the mutant eIF4E1.Fu allele and confirmed the correlation between genotype and phenotype. This study describes a novel source of resistance and an ideal co-dominant marker that can be applied in breeding for resistance to PVY and other potyviruses.

Modern Biotechnologies: Innovative and Sustainable Approaches for the Improvement of Sugarcane Tolerance to Environmental Stresses

Sugarcane (Saccharum spp.) is one of the most important industrial cash crops, contributing to the world sugar industry and biofuel production. It has been cultivated and improved from prehistoric times through natural selection and conventional breeding and, more recently, using the modern tools of genetic engineering and biotechnology. However, the heterogenicity, complex poly-aneuploid genome and susceptibility of sugarcane to different biotic and abiotic stresses represent impediments that require us to pay greater attention to the improvement of the sugarcane crop. Compared to traditional breeding, recent advances in breeding technologies (molecular marker-assisted breeding, sugarcane transformation, genome-editing and multiple omics technologies) can potentially improve sugarcane, especially against environmental stressors. This article will focus on efficient modern breeding technologies, which provide crucial clues for the engineering of sugarcane cultivars resistant to environmental stresses.

Improved nutritional quality in fruit tree species through traditional and biotechnological approaches

The increasing evidences on the relation between diet and human health are driving the consumers toward the choice of foods with high amount of nutrients, considered the molecules responsible for the regulation of several metabolic and biochemical processes, and for the prevention of many chronic diseases. Among food products, fruits represent a natural source of many different nutrients and possess much importance in a balanced diet. The increase of the micro/macronutrient levels and the decrease of antinutrients amount are considered main objectives for the improvement of fruit trees nutritional value. This review summarizes many of the attempts made to increase the nutritional quality of fruit tree species during the last decades through the application of traditional and molecular breeding technologies, and the most recent New breeding techniques (NBTs). New genotypes with improved nutritional quality have been obtained for different fruit tree species, either by increasing the content of well-known beneficial molecules, such as phenolic compounds, vitamins, and carotenoids, or by decreasing the levels of specific antinutrients. The development of molecular techniques and biotechnological tools allowed the identification and validation of candidate genes involved in the regulation of specific classes of nutritional compounds in fruit trees, and useful to obtain nutritionally improved products. NBTs represent alternative tools to classical breeding techniques, to regulate one or more fruit trees key nutrients in a more quick and precise manner. However, genetic engineering approaches still present public and regulatory concerns that strongly limit their exploitation. • Fruit consumption provides essential macro and micronutrients for human health • Conventional breeding is widely used, but presents several limitations • Molecular techniques can be applied to assist and optimize conventional breeding • New biotechnological tools allow the engineered introduction of quality traits • Genetic engineering approaches still present public and regulatory concerns

Genome‐wide SNP discovery and QTL mapping for economic traits in a recombinant inbred line of Oryza sativa

AbstractThe objective of the study was to understand the genetic basis of eight traits conferring grain appearance and yield in a recombinant inbred line (RIL8) derived from a cross between cultivated Indica rice varieties Dexiang074B and Pujiang6. We conducted whole genome re‐sequencing for the two parental lines and genotyping by sequencing (GBS) for the RIL8 population. Next, we aligned the clean reads to the rice genome Nipponbare IRGSP 1.0, constructed the genetic linkage map (GLM), and performed the quantitative trait loci (QTL) analysis. In total, 2631 high‐quality markers were generated for 315 RIL8 samples. We identified a rice GLM containing 12 linkage groups (total map distance: 1946.71 cM; average map distance: 0.74 cM) and 98 QTLs related to the rice yield, including 31 high credible QTLs. In addition, 39 QTLs were identified to be associated with the G*E interaction. While most of the QTLs were co‐localized with previously reported rice QTLs, some novel QTLs were identified for the first time in this study. These findings provide a genetic basis for developing cultivated rice with good economic characteristics based on molecular breeding technologies.

Genetic Resources of Wild Rice (Oryza rufipogon) for Biotic and Abiotic Stress Tolerance Traits

Rice (Oryza sativa L.) is the most important staple food crop of the world; nearly half of the global population depend on it for majority of their dietary intake. Many stresses (biotic and abiotic) have critically affected rice production throughout the world due to global warming, changing climatic conditions and in addition non-durability of biotic resistance gene(s) incorporated into cultivars. Yield increase is not as per the required rate and becomes yield rate is in stagnation. Primary reason of yield stagnation is due to the narrow genetic base in the released varieties. Minimum number of parental lines were utilised to develop new crop varieties which ultimately leads to narrow genetic base. The narrow genetic base in the improved varieties is going to be a main bottleneck for crop improvement program which shield the yield increase. Genetic bottleneck during domestication causes erosion of the genetic diversity in the well adapted cultivars which leads to yield stagnation. Yield plateaus can be surmount through genetic gain by combining the yield related genes/QTLs from different genetic resources of rice germplasm both from local landraces (CLR) and crop wild relatives (CWR). Wild species are the reservoir of genetic diversity with wide adaptability and tolerance to many biotic and abiotic stresses. It is utmost necessary to characterize and conserve rice germplasm for evaluation and effective use of the genetic diversity prevailed in the rice gene pool. Genetic variability in respect to biotic/abiotic resistance is inadequate in the genetic resources of cultivated rice; however, these traits specific genes are available in the unexplored wild species of Oryza which are considered as rich source of agronomically important traits including biotic/abiotic traits. Therefore, breeders are trying to identify and transfer of these valuable genes from wild Oryza species to improve varieties through pre-breeding method and with the assistance of molecular breeding technology.

Functional Analysis of Haplotypes in Bovine PSAP Gene and Their Relationship with Beef Cattle Production Traits.

Simple SummaryWith the rapid development of information technology and molecular biotechnology, animal molecular breeding technology is playing an increasingly important role in beef cattle breeding. Prosaposin (PSAP) is involved in regulating the growth and development of animals, and it is reported that PSAP is an important marker-assisted selection (MAS) in cattle herd. The purpose of this study was to explore the novel variants in 3’ UTR of cattle PSAP and evaluate their effects on the morphological traits of four Chinese cattle breeds. In this study, 13 variants were identified in the PSAP 3’ UTR from 501 individuals belonging to four cattle breeds. In Nanyang cattle, the distribution of haplotypes was different from the other three breeds. Two groups of haplotypes had association with morphological traits by changing the secondary structures of PSAP 3’ UTR rather than the miR-184 target sites. This study not only expands the genetic variation spectrum of cattle PSAP but also contributes to MAS genetics and breeding of Chinese cattle breeds.The purpose of this study was to explore functional variants in the prosaposin (PSAP) three prime untranslated region (3’ UTR) and clarify the relationship between the variants and morphological traits. Through Sanger sequencing, 13 variations were identified in bovine PSAP in four Chinese cattle breeds, with six of them being loci in 3’ UTR. In particular, Nanyang (NY) cattle had a special genotype and haplotype distribution compared to the other three breeds. NY cattle with ACATG and GCGTG haplotypes had higher morphological traits than GTACA and GTACG haplotypes. The results of dual-luciferase reporter assay showed that ACATG and GCGTG haplotypes affected the morphological traits of NY cattle by altering the secondary structure of PSAP 3’ UTR rather than the miR-184 target sites. The findings of this study could be an evidence of a complex and varying mechanism between variants and animal morphological traits and could be used to complement candidate genes for molecular breeding.

Advances in genomics of cashew tree: molecular tools and strategies for accelerated breeding

Cashew is the second most important edible tree nut crop after almonds. It is cultivated in more than 30 countries due to economic and nutritional importance. The global demand for cashew is increasing rapidly every year. Like in other perennial tree species, genetic improvement of cashew by traditional breeding is slow and unpredictable due to the long juvenile phase, high degree of heterozygosity, lack of juvenile-mature traits correlations and large size of the mature plant. Additionally, most of the yield and agronomic traits are genetically complex which complicate its breeding. Recently, the next-generation sequencing (NGS) and high-throughput genotyping technologies have expedited the pace of development of genomic tools and resources for genomics-orphan crops like cashew. The genomics advancements allow designing novel molecular breeding technologies with the potential for enhancing genetic gains and accelerating crop improvement, which is of utmost importance in the breeding of long juvenile species like cashew. In this review article, we describe the breeding objectives, advances in construction of linkage map, QTL dissection and development of genomic sequence resources in cashew. It is followed by a description of designing different genomics-based tools and strategies for accelerating the cashew breeding to quickly develop superior cultivars.

Breeding for low cadmium accumulation cereals.

Cadmium (Cd) is an element that is nonessential and extremely toxic to both plants and human beings. Soil contaminated with Cd has adverse impacts on crop yields and threatens human health via the food chain. Cultivation of low-Cd cultivars has been of particular interest and is one of the most cost-effective and promising approaches to minimize human dietary intake of Cd. Low-Cd crop cultivars should meet particular criteria, including acceptable yield and quality, and their edible parts should have Cd concentrations below maximum permissible concentrations for safe consumption, even when grown in Cd-contaminated soil. Several low-Cd cereal cultivars and genotypes have been developed worldwide through cultivar screening and conventional breeding. Molecular markers are powerful in facilitating the selection of low-Cd cereal cultivars. Modern molecular breeding technologies may have great potential in breeding programs for the development of low-Cd cultivars, especially when coupled with conventional breeding. In this review, we provide a synthesis of low-Cd cereal breeding.