Modern Breeding Research Articles

The Era of Plant Breeding: Conventional Breeding to Genomics-assisted Breeding for Crop Improvement.

Plant breeding has made a significant contribution to increasing agricultural production. Conventional breeding based on phenotypic selection is not effective for crop improvement. Because phenotype is considerably influenced by environmental factors, which will affect the selection of breeding materials for crop improvement. The past two decades have seen tremendous progress in plant breeding research. Especially the availability of high-throughput molecular markers followed by genomic-assisted approaches significantly contributed to advancing plant breeding. Integration of speed breeding with genomic and phenomic facilities allowed rapid quantitative trait loci (QTL)/gene identifications and ultimately accelerated crop improvement programs. The advances in sequencing technology helps to understand the genome organization of many crops and helped with genomic selection in crop breeding. Plant breeding has gradually changed from phenotype-to-genotype-based to genotype-to-phenotype-based selection. High-throughput phenomic platforms have played a significant role in the modern breeding program and are considered an essential part of precision breeding. In this review, we discuss the rapid advance in plant breeding technology for efficient crop improvements and provide details on various approaches/platforms that are helpful for crop improvement. This review will help researchers understand the recent developments in crop breeding and improvements.

Introduction of breeding samples of meadow clover according to economically valuable characteristics using modern breeding methods

The paper presents the results of research on the formation of complex hybrid populations, an assessment of the collection samples of clover on a complex of economically valuable traits for the creation of forage varieties. The basis for the study were promising plants that weresown in a wide row and individually in a row. By negative selection, weak and underdeveloped plants were mowed down. It`s been noticed that there was the direct dependence of clover seeds` creation from the weather conditions. The collection samples of meadow clover`s assessment was given according to the complex of economically valuable features for the creation of the hay –pasture type varieties. The best samples are allocated for the yield of the green mass, the plants` height. The initial material was obtained on the signs of adaptability, yield of green mass, foliage and seed productivity. Promising clover samples were selected for high seed productivity, reaching more than 60 %. Similarly, in accordance with the vertical zonality of the natural habitats of wild introducers, the protein content in plant samples also increases. In terms of fodder yield, the maximum indicators were noted in the varieties Farn, Ustodlivy (Belorussian selection), Orlik (All-Russian Scientific Research Institute of Legumes and Millet Crops), complex hybrid populations that exceeded the standard – the Daryal variety by 12-25%. According to seed, Nart varieties were distinguished. Synthetic populations Syn 305-03, Syn 274-94 (selection SKNIIGPSH VNC RAS), FM-143(VNII kordov), Dargavsky, (wild specimen of RSO – Alanya).

Study of genetic polymorphism of grain pea cultivars

Pea (Pisum sativum L., 1753) is an essential pulse crop of global importance, which is a source of complete high-quality protein. Breeding new pea cultivars with improved economic valuable traits and high adaptive abilities is important for increasing the production of valuable high-protein pea grain. The key role in breeding is assigned to the initial material. A decrease in the genetic diversity of the initial material of cultivated plants, including pea, has become the main problem of modern breeding. In this regard, the issue of studying and preserving the genetic polymorphism of pea is relevant. Molecular genetic markers of simple sequence repeat (SSR) are widely used for this purpose. Here we aim to (1) to assess morphobiological and economical valuable traits and (2) analyze the molecular genetic diversity of the original pea material. The object of the research work was 20 grain pea cultivars. The yield structure elements of these cultivars were evaluated, and their molecular genetic polymorphism was analyzed using SSR markers AA5, AA355, AB28, AB71, and AD147. Early-ripening and highly productive cultivars were identified; they can be recommended for use as the initial material for pea breeding. As a result of the SSR analysis, 26 polymorphic alleles were identified, on average 5.2 alleles per locus. All studied cultivars were distinguished by a unique combination of alleles at five microsatellite loci, which allowed them to be identified. Based on the data of molecular genetic analysis, a cluster analysis was carried out, and a dendrogram was constructed. On the dendrogram, the studied cultivars were grouped according to the features of their morphological and economically valuable traits.

Evaluation of functional kompetitive allele-specific PCR (KASP) markers for selection of drought-tolerant wheat (Triticum aestivum) genotypes.

Wheat (Triticum aestivum ) is a major crop around the globe and different techniques are being used for its productivity enhancement. Germplasm evaluation to improve crop productivity mainly depends on accurate phenotyping and selection of genotypes with a high frequency of superior alleles related to the trait of interest. Therefore, applying functional kompetitive allele-specific PCR (KASP) markers for drought-related genes is essential to characterise the genotypes for developing future climate-resilient wheat crop. In this study, eight functional KASP markers and nine morphological traits were employed to evaluate the 40 wheat genotypes for drought tolerance. Morphological traits showed significant variation (P ≤0.05) among the genotypes, except tiller count (TC), fresh root weight (FRW) and dry root weight (DRW). PCA biplot showed that 63.3% phenotypic variation was explained by the first two PCs under control treatment, while 70.8% variation was explained under drought treatment. It also indicated that root length (RL) and primary root (PR) have considerable variations among the genotypes under both treatments and are positively associated with each other. Hence, the findings of this study suggested that both these traits could be used as a selection criterion to classify the drought-tolerant wheat genotypes. KASP genotyping accompanied by morphological data revealed that genotypes Markaz, Bhakar Star, China 2, Aas and Chakwal-50 performed better under drought stress. These outperforming genotypes could be used as parents in developing drought-tolerant wheat genotypes. Hence, KASP genotyping assay for functional genes or significant haplotypes and phenotypic evaluation are prerequisites for a modern breeding program.

Characterization of wheat-Thinopyrum bessarabicum genetic stock for stripe rust and Karnal bunt resistance.

Utilization of modern breeding techniques for developing high yielding and uniform plant types ultimately narrowing the genetic makeup of most crops. Narrowed genetic makeup of these crops has made them vulnerable towards disease and insect epidemics. For sustainable crop production, genetic variability of these crops must be broadened against various biotic and abiotic stresses. One of the ways to widen genetic configuration of these crops is to identify novel additional sources of durable resistance. In this regard crops wild relatives are providing valuable sources of allelic diversity towards various biotic, abiotic stress tolerance and quality components. For incorporating novel variability from wild relative's wide hybridization technique has become a promising breeding method. For this purpose, wheat-Th. bessarabicum amphiploid, addition and translocation lines have been screened in field and screen house conditions to get novel sources of yellow rust and Karnal bunt resistant. Stripe rust screening under field conditions has revealed addition lines 4JJ and 6JJ as resistant to moderately resistant while addition lines 3JJ, 5JJ, 7JJ and translocation lines Tr-3, Tr-6 as moderately resistant wheat-Thinopyrum-bessarabicum genetic stock. Karnal bunt screening depicted addition lines 5JJ and 4JJ as highly resistant genetic stock. These genetic stocks may be used to introgression novel stripe rust and Karnal bunt resistance from the tertiary gene pool into susceptible wheat backgrounds.

Экологические особенности Pinus sylvestris L. и видов рода Populus L. в озеленении Благовещенска (Амурская область)

This study evaluates the efficiency of phosphorus absorption from soil and fertilizers by modern varieties of oats of Tyumen selection. The studies were carried out in field and laboratory conditions. The scheme of the experiment provided for options with the introduction of increasing doses of mineral fertilizers, calculated for the planned yield from 3.0 to 6.0 t / ha. The following doses of fertilizers were applied in the experiment: N60P20; N90P40; N150P60; N200P80 kg/ha of active substance. The option without mineral fertilizers was taken as a control. Varieties of oats were sown: Talisman; Otrada; Foma. During three-year experiments, it was found that the phosphorus content in the grain of the studied varieties of oats is 0.86–1.11%; in straw - 0.26-0.27%. The application of mineral fertilizers increases the phosphorus content in the grain to 0.97-1.15%. The phosphorus content in straw increases only with the addition of N150P60 and N200P80 kg /ha – 0.47-0.53%. In the absence of fertilizers, the economic removal of phosphorus is for the variety: Talisman – 20 kg / ha; Otrada and Foma – 28 kg/ ha. With an increase in the level of mineral nutrition of household takeaways increases to 95 kg / ha. Varietal features are manifested only when fertilizers are applied at doses of N90P40 and N150P60 kg/ha. For the formation of 1 ton of grain in the absence of fertilizers, 12-14 kg of phosphorus is required. The application of fertilizers for the planned yield of up to 4.0 t / ha of grain does not affect the specific removal of phosphorus. Further increase in the level of mineral nutrition (N150P60 and N200P80) increases the specific removal to 17-19 kg / t of grain. This indicator mainly depends on the level of mineral nutrition and to a lesser extent on the varietal characteristics of oats. The use of the element balance method for the planned yield of oats ensures maximum absorption of nutrients from fertilizers - the balance coefficient of phosphorus use from fertilizers is more than 100%, while the bulk of the crop is formed due to the active consumption of soil phosphates. Scientific novelty. It was found that the Foma oat variety most effectively absorbs phosphorus from fertilizers and soil, relative to the standard Talisman variety. Keywords: AGROCHEMISTRY OF OATS; ECONOMIC REMOVAL, COEFFICIENTS OF USE FROM FERTILIZER, CHEMICAL COMPOSITION OF GRAIN, VARIETAL AGROTECHNICS, MODERN BREEDING, PLANNED YIELD, SPECIFIC PHOSPHORUS REMOVAL, LEVEL OF MINERAL NUTRITION, FERTILIZERS

CURRENT SITUATION AND PROSPECTS OF COTTON PRODUCTION IN PAKISTAN

Pakistan is the world's fifth-largest cotton producer. It is grown largely for fibre, and its oil is used as a vegetable oil and contributes significantly to the local oil industry. Cottonseed oil meets 18.1% of Pakistan's edible oil needs. In 2030, there will be 5.5 million tonnes of total demand for this purpose, with 2 million tonnes of local supply. Bt cotton, which was introduced in 2010 to remove three harmful lepidopteran insects, currently accounts for more than 90% of all cotton grown in Pakistan. Pakistan offers a lot of potential for organic cotton cultivation, particularly in unconventional cotton-growing locations with low insect burdens. Climate change-induced high temperatures and water scarcity are a big worry because contemporary agriculture is practiced in areas that already experience very high temperatures. Phenotypic selection in breeding is ineffective in creating stress-tolerant cotton. Marker-assisted selection technologies have considerably increased the effectiveness of traditional breeding. Modern breeding techniques contributed to the development of novel cotton breeding strategies. Furthermore, CRISPR/Cas9 and genome editing can establish a good foundation for improving resistance against biotic and abiotic stresses.

SPEED BREEDING AND ITS IMPORTANCE FOR THE IMPROVEMENT OF AGRICULTURAL CROPS

Current environmental changes and continued global population growth represent a significant concern for food security. The slow rate at which current plant breeding programs are progressing is partly attributed to the long generation time of plants during the breeding process. One solution to overcome this obstacle is the use of Speed breeding technology that shortens the generation time to accommodate multiple generations of crops per year and accelerates crop research. The term "Speed breeding" was coined by Australian researchers in 2003 and is inspired by NASA experiments performed on a space mission. In this context, this paper summarizes some of the technological aspects, opportunities and limitations associated with Speed breeding. The integration of Speed breeding with other modern breeding technologies can further reduce the breeding cycle time and make selection for some novel traits more effective. Speed breeding is an innovative and promising breeding technology to ensure food security, which accelerates the development and release of new crop varieties.

Identification of Genetic Markers and Genes Putatively Involved in Determining Olive Fruit Weight.

The fruit size of a cultivated olive tree is consistently larger than its corresponding wild relatives because fruit size is one of the main traits associated with olive tree domestication. Additionally, large fruit size is one of the main objectives of modern olive breeding programs. However, as the long juvenile period is one main hindrance in classic breeding approaches, obtaining genetic markers associated with this trait is a highly desirable tool. For this reason, GWAS analysis of both genetic markers and the genes associated with fruit size determination, measured as fruit weight, was herein carried out in 50 genotypes, of which 40 corresponded to cultivated and 10 to wild olive trees. As a result, 113 genetic markers were identified, which showed a very high statistically significant correlation with fruit weight variability, p < 10−10. These genetic markers corresponded to 39 clusters of genes in linkage disequilibrium. The analysis of a segregating progeny of the cross of “Frantoio” and “Picual” cultivars allowed us to confirm 10 of the 18 analyzed clusters. The annotation of the genes in each cluster and the expression pattern of the samples taken throughout fruit development by RNAseq enabled us to suggest that some studied genes are involved in olive fruit weight determination.

Root volatile profiles and herbivore preference are mediated by maize domestication, geographic spread, and modern breeding

Domestication affected the abundances and diversity of maize root volatiles more than northward spread and modern breeding, and herbivore preference for roots was correlated with volatile diversity and herbivore resistance. Studies show that herbivore defenses in crops are mediated by domestication, spread, and breeding, among other human-driven processes. They also show that those processes affected chemical communication between crop plants and herbivores. We hypothesized that (i) preference of the herbivore (Diabrotica virgifera virgifera) larvae for embryonic roots of maize (Zea mays mays) would increase and (ii) root volatile diversity would decrease with the crop's domestication, northward spread to present-day USA, and modern breeding. We used Balsas teosinte (Zea mays parviglumis), Mexican and USA landrace maizes, and US inbred maize lines to test these hypotheses. We found that herbivore preference and volatile diversity increased with maize domestication and northward spread but decreased with modern breeding. Additionally, we found that the abundances of single volatiles did not consistently increase or decrease with maize domestication, spread, and breeding; rather, volatiles grouped per their abundances were differentially affected by those processes, and domestication had the greatest effects. Altogether, our results suggested that: the herbivore's preference for maize roots is correlated with volatile diversity and herbivore resistance; changes in abundances of individual volatiles are evident at the level of volatile groups; and maize domestication, but not spread and breeding, affected the abundances of some green leaf volatiles and sesquiterpenes/sesquiterpenoids. In part, we discussed our results in the context of herbivore defense evolution when resources for plant growth and defense vary across environments. We suggested that variability in relative abundance of volatiles may be associated with their local, functional relevance across wild and agricultural environments.

QTL and Candidate Genes: Techniques and Advancement in Abiotic Stress Resistance Breeding of Major Cereals.

At least 75% of the world's grain production comes from the three most important cereal crops: rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays). However, abiotic stressors such as heavy metal toxicity, salinity, low temperatures, and drought are all significant hazards to the growth and development of these grains. Quantitative trait locus (QTL) discovery and mapping have enhanced agricultural production and output by enabling plant breeders to better comprehend abiotic stress tolerance processes in cereals. Molecular markers and stable QTL are important for molecular breeding and candidate gene discovery, which may be utilized in transgenic or molecular introgression. Researchers can now study synteny between rice, maize, and wheat to gain a better understanding of the relationships between the QTL or genes that are important for a particular stress adaptation and phenotypic improvement in these cereals from analyzing reports on QTL and candidate genes. An overview of constitutive QTL, adaptive QTL, and significant stable multi-environment and multi-trait QTL is provided in this article as a solid framework for use and knowledge in genetic enhancement. Several QTL, such as DRO1 and Saltol, and other significant success cases are discussed in this review. We have highlighted techniques and advancements for abiotic stress tolerance breeding programs in cereals, the challenges encountered in introgressing beneficial QTL using traditional breeding techniques such as mutation breeding and marker-assisted selection (MAS), and the in roads made by new breeding methods such as genome-wide association studies (GWASs), the clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system, and meta-QTL (MQTL) analysis. A combination of these conventional and modern breeding approaches can be used to apply the QTL and candidate gene information in genetic improvement of cereals against abiotic stresses.

Comparative Silk Transcriptomics Illuminates Distinctive Impact of Artificial Selection in Silkworm Modern Breeding.

Early domestication and the following improvement are two important processes in the cocoon silk evolution of silkworms. In contrast to early domestication, understanding of the improvement process is still fuzzy. By systematically comparing the larval silk gland transcriptomes of the wild, early domestic, and improved silkworms, we highlighted a novel landscape of transcriptome in the silk glands of improved ones. We first clarified that silk cocoon protein genes were up-regulated in modern breeding but not in early domestication. Furthermore, we found that differentially expressed genes (DEGs) between improved and early domestic silkworms (2711), as well as between improved and wild silkworms (2264), were obviously more than those between the early domestic and wild silkworms (158), with 1671 DEGs specific in the improved silkworm (IS-DEGs). Hierarchical clustering of all the DEGs consistently indicated that improved silkworms were significantly diverged from the early domestic and wild silkworms, suggesting that modern breeding might cause prompt and drastic dynamic changes of gene expression in the silk gland. We further paid attention to these 1671 IS-DEGs and were surprised to find that down-regulated genes were enriched in basic organonitrogen compound biosynthesis, RNA biosynthesis, and ribosome biogenesis processes, which are generally universally expressed, whereas those up-regulated genes were enriched in organonitrogen compound catabolic processes and functions involving in the dynamic regulation of protein post-translation of modification. We finally highlighted one candidate improvement gene among these up-regulated IS-DEGs, i.e., GDAP2, which may play roles in silk behavior and the overall robustness of the improved silkworm. The findings strongly suggest that modern breeding may facilitate effective control of the basic consumption of nitrogen and a stronger switch of nitrogen resources from other tissues to the silk glands, for an efficient supply for silk production, and implies the importance of brain behavior and robustness in silk yield improvement of modern breeding.

Breeding and Deploying Multiple Stress-Tolerant Maize Varieties in the Tropics

Maize is the key crop for food, feed, and nutritional security of millions of smallholder farmers and consumers in the developing world, especially in sub-Saharan Africa (SSA), Asia, and Latin America. CIMMYT and partners have adopted innovative approaches over the last one decade to develop, evaluate, and deliver elite stress-resilient and nutritionally enriched maize varieties with relevant client-preferred traits, especially in the stress-prone tropics. Effective integration of modern breeding tools and strategies, including high-throughput and precision phenotyping, doubled haploid (DH) technology, and genomics-assisted breeding, are integral part of these efforts leading to impressive genetic gains, while enhancing the pace, precision, and efficiency of breeding pipelines. Through extensive public-private partnerships, CGIAR-derived climate-resilient and multiple stress-tolerant improved maize varieties are being deployed in over 13 countries in SSA, four countries in South Asia, and several countries across Latin America. Certified seed production of CGIAR-derived improved stress-tolerant maize varieties was estimated to cover approximately 7.2 million hectares in SSA in 2022, reaching an estimated 7.2 million households, and benefitting 44 million people. In the past five years, a total 20 high-yielding drought and heat stress-tolerant maize hybrids were released in South Asia, including four new hybrids in 2022 – BWMRI-2 in Bangladesh; Rampur Hybrid-12 in Nepal; and IMH-222 and IMH-223 in India. In collaboration with seed company partners, certified seed production of climate-resilient maize hybrids scaled-up from a baseline of just 70 MT in 2018-19 to 1026 MT in 2021-22, and deployed in about 50,000 hectares in various stress-vulnerable targeted ecologies in Bangladesh, India, Nepal and Pakistan, reaching 128,200 farm families. Experiences of CIMMYT strongly indicate that besides strengthening the seed sector, adoption of progressive seed laws and regulations, are vital for improving smallholder farmers’ access to climate-resilient improved seed. Policy support and institutional innovations are also required for overcoming key bottlenecks affecting maize seed value chain.

Fighting Death for Living: Recent Advances in Molecular and Genetic Mechanisms Underlying Maize Lethal Necrosis Disease Resistance.

Maize Lethal Necrosis (MLN) disease, caused by a synergistic co-infection of maize chlorotic mottle virus (MCMV) and any member of the Potyviridae family, was first reported in EasternAfrica (EA) a decade ago. It is one of the most devastating threats to maize production in these regions since it can lead up to 100% crop loss. Conventional counter-measures have yielded some success; however, they are becoming less effective in controlling MLN. In EA, the focus has been on the screening and identification of resistant germplasm, dissecting genetic and the molecular basis of the disease resistance, as well as employing modern breeding technologies to develop novel varieties with improved resistance. CIMMYT and scientists from NARS partner organizations have made tremendous progresses in the screening and identification of the MLN-resistant germplasm. Quantitative trait loci mapping and genome-wide association studies using diverse, yet large, populations and lines were conducted. These remarkable efforts have yielded notable outcomes, such as the successful identification of elite resistant donor lines KS23-5 and KS23-6 and their use in breeding, as well as the identification of multiple MLN-tolerance promising loci clustering on Chr 3 and Chr 6. Furthermore, with marker-assisted selection and genomic selection, the above-identified germplasms and loci have been incorporated into elite maize lines in a maize breeding program, thus generating novel varieties with improved MLN resistance levels. However, the underlying molecular mechanisms for MLN resistance require further elucidation. Due to third generation sequencing technologies as well functional genomics tools such as genome-editing and DH technology, it is expected that the breeding time for MLN resistance in farmer-preferred maize varieties in EA will be efficient and shortened.

Improvement of Anther Culture to integrate Doubled Haploid Technology in Temperate Rice (Oryza sativa L.) Breeding.

Doubled haploid (DH) plant production, such as anther culture (AC), is an effective tool used in modern rice breeding programs. The improved efficient protocols applied can shorten the process of breeding. The effect of combinations of plant growth regulators (2.5 mg/L NAA, 1 mg/L 2,4-D and 0.5 mg/L kinetin; 2 mg/L 2,4-D and 0.5 mg/L BAP) in the induction medium were compared in AC for five rice breeding materials and combinations. Induction of calli ranged from 264.6 ± 67.07 to 468.8 ± 123.2 calli/100 anthers in AC of rice genotypes. Two basal media (MS and N6) and two combinations of growth regulators (1 mg/L NAA, 1 mg/L BAP and 1 mg/L kinetin; 1.5 mg/L BAP, 0.5 mg/L NAA and 0.5 mg/L kinetin) were used as regeneration media. The in vitro green plant production was the highest with the application of the N6NDK induction medium (NAA, 2,4-D and kinetin) and the MS-based regeneration medium (1 mg/L NAA, 1 mg/BAP and 1 mg/L kinetin) in anther culture of the '1009' genotype (95.2 green plantlets/100 anthers). The mean of five genotypes was 24.48 green plantlets/100 anthers for the best treatment. Flow cytometric analyses conducted identified the microspore origin of the haploid calli produced in AC, while the uniformity of spontaneous DH plants was checked in the DH1 and DH2 generations. Spontaneous chromosome doubling ranged from 38.1% to 57.9% (mean 42.1%), depending on the breeding source. The generated and selected DH lines were tested in micro- and small-plot field experiments to identify promising lines for a pedigree breeding program. The improved AC method was integrated in a Hungarian temperate rice pedigree breeding program.

Improving Coconut Using Modern Breeding Technologies: Challenges and Opportunities.

Coconut (Cocos nucifera L.) is a perennial palm with a wide range of distribution across tropical islands and coastlines. Multitude use of coconut by nature is important in the socio-economic fabric framework among rural smallholders in producing countries. It is a major source of income for 30 million farmers, while 60 million households rely on the coconut industry directly as farm workers and indirectly through the distribution, marketing, and processing of coconut and coconut-based products. Stagnant production, inadequate planting materials, the effects of climate change, as well as pests and diseases are among the key issues that need to be urgently addressed in the global coconut industry. Biotechnology has revolutionized conventional breeding approaches in creating genetic variation for trait improvement in a shorter period of time. In this review, we highlighted the challenges of current breeding strategies and the potential of biotechnological approaches, such as genomic-assisted breeding, next-generation sequencing (NGS)-based genotyping and genome editing tools in improving the coconut. Also, combining these technologies with high-throughput phenotyping approaches and speed breeding could speed up the rate of genetic gain in coconut breeding to solve problems that have been plaguing the industry for decades.

Agriculture and food security under a changing climate: An underestimated challenge.

Pathways to eradicate global hunger while bending the curve of biodiversity loss unanimously suggest changing to less energy-rich diets, closing yield gaps through agroecological principles, adopting modern breeding technologies to foster stress resilience and yields, as well as minimizing harvest losses and food waste. Against the background of a brief history of global agriculture, we review the available evidence on how the global food system might look given a global temperature increase by 3°. We show that a moderate gain in the area suitable for agriculture is confronted with substantial yield losses through strains on crop physiology, multitrophic interactions, and more frequent extreme events. Self-amplifying feedback are unresolved and might lead to further losses. In light of these uncertainties, we see that complexity is underestimated and more systemic research is needed. Efficiency gains in agriculture, albeit indispensable, will not be enough to achieve food security under severe climate change.

The Gossypium herbaceum L. Wagad genome as a resource for understanding cotton domestication.

Gossypium herbaceum is a species of cotton native to Africa and Asia that is one of the 2 domesticated diploids. Together with its sister-species G. arboreum, these A-genome taxa represent models of the extinct A-genome donor of modern polyploid cotton, which provide about 95% of cotton grown worldwide. As part of a larger effort to characterize variation and improve resources among diverse diploid and polyploid cotton genomes, we sequenced and assembled the genome of G. herbaceum cultivar (cv.) Wagad, representing the first domesticated accession for this species. This chromosome-level genome was generated using a combination of PacBio long-read technology, HiC, and Bionano optical mapping and compared to existing genome sequences in cotton. We compare the genome of this cultivar to the existing genome of wild G. herbaceum subspecies africanum to elucidate changes in the G. herbaceum genome concomitant with domestication and extend these analyses to gene expression using available RNA-seq. Our results demonstrate the utility of the G. herbaceum cv. Wagad genome in understanding domestication in the diploid species, which could inform modern breeding programs.

Challenges and Opportunities in Genetic Improvement of Essential Oil-Bearing Damask Rose (Rosa damascena): A Review

Damask rose cultivated for essential oil production mainly used in perfume industry. Due to the highly perishable flowers, post-harvest handling of the flowers prior to oil extraction would be considered as a key point in rose essential oil production. Besides its major application in aroma and cosmetic industries, rose essential oil has been reported with valuable pharmacological properties such as antibacterial, antioxidant, and cytotoxic activities. Plant breeders are being encouraged to develop new damask rose cultivars with improved oil content and higher flower yield qualities due to rising market demand. The aforementioned qualities can be improved using traditional breeding methods such as clonal selection and intra-specific hybridization. But, through the convention breeding method creation of genetic variation is time taking, and the preservation of the authentic scent and quality of the rose oil is very difficult. Recent breakthroughs in molecular-markers techniques, genomics, and transcriptomics, have resulted in large volumes of data being generated in damask rose. Several attempts have been undertaken to accelerate the breeding of R.damascena using molecular technologies. However, due to the species' high heterozygosity and polyploidy nature, translating the findings of such studies to practical breeding remains a significant challenge. This review paper outlines recent advances in conventional and modern molecular breeding procedures, as well as their potential uses and limitations in improving the oil-bearing rose.

Increasing plant group productivity through latent genetic variation for cooperation.

Historic yield advances in the major crops have, to a large extent, been achieved by selection for improved productivity of groups of plant individuals such as high-density stands. Research suggests that such improved group productivity depends on "cooperative" traits (e.g., erect leaves, short stems) that-while beneficial to the group-decrease individual fitness under competition. This poses a problem for some traditional breeding approaches, especially when selection occurs at the level of individuals, because "selfish" traits will be selected for and reduce yield in high-density monocultures. One approach, therefore, has been to select individuals based on ideotypes with traits expected to promote group productivity. However, this approach is limited to architectural and physiological traits whose effects on growth and competition are relatively easy to anticipate. Here, we developed a general and simple method for the discovery of alleles promoting cooperation in plant stands. Our method is based on the game-theoretical premise that alleles increasing cooperation benefit the monoculture group but are disadvantageous to the individual when facing noncooperative neighbors. Testing the approach using the model plant Arabidopsis thaliana, we found a major effect locus where the rarer allele was associated with increased cooperation and productivity in high-density stands. The allele likely affects a pleiotropic gene, since we find that it is also associated with reduced root competition but higher resistance against disease. Thus, even though cooperation is considered evolutionarily unstable except under special circumstances, conflicting selective forces acting on a pleiotropic gene might maintain latent genetic variation for cooperation in nature. Such variation, once identified in a crop, could rapidly be leveraged in modern breeding programs and provide efficient routes to increase yields.