Breeding Improvement Research Articles

Systematic literature review of Hyphessobrycon eques: A support for the improvement of captive breeding

Hyphessobrycon eques has a great prominence in fishkeeping and scientific research. In this context, a systematic literature review was performed to assist in the improvement of captive breeding of this species and to identify knowledge gaps. Notably, of the 966 articles published between 1997 and 2020 found in an initial screening of the digital libraries of Google Scholar, PubMed, SciELO, Science Direct, and Scopus, only 56 represented research on the species according to the established criteria. Considering aspects pertinent to captive reproduction, 25 studies were selected. These studies addressed information regarding reproduction; embryonic, larval, and juvenile development of the species; parasitic fauna; limiting concentrations of prophylactic agents; food preferences; and dietary supplements already used for these fish. Only seven studies reported information on the physicochemical characteristics of water in natural habitats, with great variations in several parameters, mainly those related to temperature. In 5 of the 25 selected studies, information related to reproductive characteristics and/or embryonic, larval, and juvenile development was addressed. However, only two studies developed experimental studies with information relevant to the captive breeding of the species. Studies to identify parasitic fauna and to analyze the use of prophylactic agents were also found. As for the information gaps on the cultivation of the species, there are no studies related to nutrition seeking to determine the species nutritional needs, including feeding frequencies, feeding durations, and specific amounts of food. Therefore, this review offers a great support for the breeding of H. eques by highlighting opportunities for new scientific studies that could enrich and collaborate in the breeding of this ornamental fish.

Genome wide association study on development and evolution of glutinous rice

BackgroundGlutinous rice as a special endosperm type is consumed as a staple food in East Asian countries by consumers’ preference. Genetic studies on glutinous rice could be conducive to improve rice quality and understand its development and evolution. Therefor, we sought to explore more genes related to glutinous by genome wide association study and research the formation history for glutinous.ResultsHere, genome-wide association study was performed to explore the associated loci/genes underlying glutinous rice by using 2108 rice accessions. Combining the expression patterns analysis, 127, 81, and 48 candidate genes were identified to be associated with endosperm type in whole rice panel, indica, and japonica sub-populations. There were 32 genes, including three starch synthesis-related genes Wx, SSG6, and OsSSIIa, detected simultaneously in the whole rice panel and subpopulations, playing important role in determining glutinous rice. The combined haplotype analyses revealed that the waxy haplotypes combination of three genes mainly distributed in Southeast Asia (SEA), SEA islands (SER) and East Asia islands (EAR). Through population structure and genetic differentiation, we suggest that waxy haplotypes of the three genes firstly evolved or were directly inherited from wild rice in japonica, and then introgressed into indica in SER, SEA and EAR.ConclusionsThe cloning and natural variation analysis of waxy-related genes are of great significance for the genetic improvement of quality breeding and comprehend the history in glutinous rice. This work provides valuable information for further gene discovery and understanding the evolution and formation for glutinous rice in SEA, SER and EAR.

The effectiveness of treatment for dirofilariasis in dogs

Livestock industry – dog breeding is of great importance in human activities. Infectious and invasive diseases are a deterrent to the breeding and improvement of dog breeds. Not only do they cause significant economic damage to dog breeding, but they can also be dangerous to humans. Such diseases include dirofilariasis – an invasive disease that is transmitted through intermediate hosts – blood-sucking mosquitoes. The urgency of dirofilariasis is also due to the difficulties of therapy, because effective drugs of imported production are not available due to high cost, and the arsenal of domestic counterparts is small. The aim of the study was to establish the effectiveness of various treatment regimens for dog dirofilariasis. For this purpose, dogs infected with Dirofilaria immitis used specific drugs immiticide (AS – melarsomin), stronghold (AS – selamectin), doxycyl (AS – doxycyclini hydrochloridum), advocate (AS – imidacloprid, moxidectin). The main indicators of the effect of drugs were extensefficiency and intensefficiency. Studies have shown that with the intensity of microdirofilariasic invasion below 20 larvae in 1 cm3 of dog blood and in the absence of clinical manifestations of the disease extensefficiency and intensefficiency of concomitant use of immiticide and stronghold, doxycyl and stronghold, immiticide and advocate, doxycyl and advocate on the 15th day of the experiment was 100.0 %, 100.0 %, 100.0 %, 83.33 and 86.81 % respectively. With the intensity of microdirofilariasic invasion from 20 to 40 larvae in 1 cm3 of dog blood, the extensefficiency and intensefficiency of the proposed treatment regimens were respectively 100.0 %, 83.33 and 88.46 %, 66.66 and 82.54 %, 66.66 and 80.20 %. On the 180th day of treatment and during the year in all experimental groups of dogs, regardless of the intensity of the invasion of microdirofilariae in the blood of animals were not detected. Immunochromatographic rapid test, starting from 30 days of the experiment, was negative for adult females of D. immitis. The results of the research allow us to recommend the proposed treatment regimens in the effective control of dog dirofilariasis caused by D. immitis.

Ectopic expression of BrIQD35 promotes drought stress tolerance in Nicotiana benthamiana.

The plant IQD gene family is responsive to a variety of stresses. In this study, we studied the structural features and functions of the gene BrIQD35 in Chinese cabbage, a member of the IQD gene family. BrIQD35 was cloned and shown to contain an IQ motif. Transient expression of BrIQD35 indicated that it was localized on the plasma membrane and was significantly upregulated under drought and salt stress in Chinese cabbage. To further identify the function of BrIQD35, it was heterologously overexpressed in Nicotiana benthamiana. Although there was no significant difference between BrIQD35-overexpressed and wild-type (WT) plants under salt stress, WT N. benthamiana showed more wilting than the BrIQD35-overexpressed plants under drought stress. Since the IQ motif has been annotated as a CaM binding site, yeast two-hybrid assays were used to explore the interaction between BrIQD35 and CaM. The results indicated that BrIQD35 interacts weakly with CaMb, but not with CaMa, suggesting that BrIQD35 may function through the Ca2+ -CaMb pathway. The findings reveal a novel gene involved in drought tolerance, which is important for plant breeding and quality improvement for Chinese cabbage.

Myth and reality of a global crisis for agricultural pollination

Mounting evidence shows that pollinators are declining as a result of widespread environmental degradation. This loss raises concerns that a global pollination crisis could threaten the human food supply by decreasing crop yield and even promote famine under a hypothetical scenario of total pollinator extinction. This catastrophic possibility has prompted intense interest from scientists, politicians and the general public. However, three lines of evidence do not support such an apocalyptic scenario. First, even though the abundance and diversity of wild pollinators are declining worldwide, the global population of managed honey-bee hives has increased by ~80% since the early 1960s. Second, agricultural production would decrease by <10% in the total absence of bees because relatively few crops are completely pollinator dependent. Lastly, despite widespread pollination deficits, current evidence is inconsistent with deceleration in yield growth with increasing pollinator dependence at a global scale, probably due to improvements in crop breeding and external agricultural subsidies. Overall, this evidence refutes simplistic claims of human starvation caused by a hypothetical total pollinator extinction. Nevertheless, pollination problems may loom. Although pollinators are responsible for a minor fraction of global agriculture production, this fraction has increased ~600% since 1961, greatly outpacing human population growth and the growth of the global population of managed honey bees. This large production increase is explained to a considerable extent by the rapid expansion of pollinator-dependent monocultures at the expense of natural and diverse agricultural habitats. By driving pollinator decline, this land-use transformation could worsen pollination deficits and promote further crop expansion given sustained market demands. Therefore, although the human food supply is not currently subject to a global pollination crisis, a spiralling positive-feedback between the impacts of agriculture expansion and pollinator decline on crop yield could accelerate precipitous biodiversity loss by promoting further habitat destruction and homogenization.

Comparative Analysis of the Effects of Internal Factors on the Floral Color of Four Chrysanthemum Cultivars of Different Colors

Flower color, a critical phenotypic trait of ornamental plants, is an essential indicator for flower variety classification. Many physical and internal factors that affect flower color have been widely investigated; however, the effects of internal factors during the flowering period remain unknown. In this study, we evaluated the effects of internal factors on floral coloration during the flowering period of four chrysanthemum cultivars of different colors. colorimetric measurements showed that L*, a*, and b* were in correlation with the lightness and color development in the four chrysanthemum cultivars. The distinctive shape of upper epidermal cells was observed in each flowering stage of different colored chrysanthemums. With progression of the flowering process, the content of anthocyanins and carotenoids increased during early stages, decreased at the senescence stage, and was the highest at the full-bloom stage. The vacuolar pH of flowers gradually decreased as the flower bloomed. Metal contents in flowers varied across different chrysanthemum varieties. Anthocyanins biosynthesis genes, such as CmCHS and CmCHI, were expressed and responsible for pigment changes in red chrysanthemums. Moreover, the expression pattern of cytosol pH-related genes, such as CmVHA-a1, CmVHA-C, and CmVHA-C″1, was in accordance with a decrease in pH during flowering stages. Our results revealed the effects of main internal factors on floral color during the flowering period in four Chrysanthemum varieties, providing insights into the introcellular and molecular regulatory mechanisms of flower coloration and laying key foundations for the improvement of color breeding in chrysanthemums.

Integrated Transcriptomic and Metabolomic Analyses Reveal the Mechanisms Underlying Anthocyanin Coloration and Aroma Formation in Purple Fennel.

The color and aroma are the significant traits of vegetables and fruits, but the metabolic and molecular mechanisms underlying anthocyanin accumulation and aroma formation remain almost unknown in fennel (Anethum foeniculum L.), which is a crucial vegetable crop and grown widely for aromatic leaves and bulbs. Here, ten major anthocyanins identified and quantified by ultra-high performance liquid chromatography coupled with quadrupole Orbitrap high-resolution mass spectrometry (UHPLC-Q-Orbitrap HRMS) were mainly responsible for the coloration of purple fennel leaf. With the application of GC-MS, it was found that the reduced volatile phenylpropanoids including isoeugenol, trans-isoeugenol, and apiol chiefly account for the characteristic aroma changes of the purple fennel. Moreover, the characteristic anthocyanin coloration and aroma formation in purple fennel were systematically studied with the integrated transcriptomics and metabolomics. The critical genes associated with the biosynthesis and regulation of anthocyanins and volatile phenylpropanoids were isolated and studied carefully in transiently transfected tobacco cells and transgenic tomato plants. Together with the results of UHPLC-Q-Orbitrap HRMS, RT-qPCR, and yeast two hybrid (Y2H), it is proved that the metabolic flux redirection of phenylpropanoid pathway primarily regulated by a functional MYB-bHLH-WD40 complex consisting of AfTT8, AfMYB7, and AfTTG1 accounts for the characteristic anthocyanin coloration and aroma formation in purple fennel leaf. The systematic understanding of the anthocyanin accumulation and aroma formation will assist in the improvement of fennel resource utilization and breeding.

Integrative analysis of metabolome and transcriptome reveals the improvements of seed quality in vegetable soybean (Glycine max (L.) Merr.)

Vegetable soybean is derived from grain soybean. Seeds of vegetable soybean are bigger, sweeter, and have smoother texture and better flavor than those of grain soybean. To better understand the improvements of seed quality in vegetable soybean, comparative metabolome and transcriptome analyses were performed in the developing seeds between grain (Williams 82) and vegetable (Jiaoda 133) soybeans. A total of 299 differential metabolites were identified between two genotypes, with an increase in free amino acids, carbohydrates, sterols, and flavonoids and a decrease in fatty acid in vegetable soybean. Thousands of differentially expressed genes (DEGs) were identified by transcriptome analysis. DEGs were used for weighted gene co-expression network analysis (WGCNA), yielding 16 co-expression modules. The expression patterns of DEGs within these modules were distinct between two genotypes. Functional enrichment analysis revealed that metabolic pathways, including alanine, aspartate and glutamate metabolism, fatty acid degradation, starch and sucrose metabolism, sucrose transport, and flavonoid biosynthesis, were up-regulated, whereas photosynthesis, arginine biosynthesis, arginine and proline metabolism, glycolysis/gluconeogenesis, and fatty acid biosynthesis were down-regulated in vegetable soybean. Reasonably, the alterations of metabolic pathways corresponding to DEGs partly explained the formation of differential metabolites. These findings provide a better understanding of seed development and breeding improvements of vegetable soybean.

Genomic analysis of 10 years of artificial selection in community-based breeding programs in two Ethiopian indigenous sheep breeds.

In recent times, community-based breeding programs (CBBPs) have been advocated as the best strategy for genetic improvement of local breeds in smallholder farms in developing countries. Since 2009, CBBPs have been implemented for Ethiopian Bonga and Menz sheep to improve growth rates resulting in significant genetic gains in 6-month weights. With the hypothesis that selection could be impacting their genomes, we systematically screened for possible genome changes in the two breeds by analyzing 600K BeadChip genotype data of 151 individuals (with the highest breeding values for 6-month weights) from CBBP flocks against 98 individuals from non-CBBP flocks. We observed no differences in genetic diversity and demographic dynamics between CBBP and non-CBBP flocks. Selection signature analysis employing ROH, logistic regression genome-wide association study , FST , XP-EHH and iHS revealed 5 (Bonga) and 11 (Menz) overlapping regions under selection, that co-localized with QTLs for production (body size/weight, growth, milk yield), meat/milk quality, and health/parasite resistance, suggesting that the decade-long selection has likely started to impact their genomes. However, genome-wide genetic differentiation between the CBBP and non-CBBP flocks is not yet clearly evident.

Development of a new genetic method of improving the Mulberry Silkworm Bombyx Mori L. breed balanced on Embryonic Z-Lethal

The problem of artificial control of sex has become important for the genetics and selection of many beneficial animals, which has not lost its relevance even in the current period. This article reveals the results of research on the improvement of the unique C-8ngl breed of Bombyx Mori L. mulberry silkworm balanced on embryonic Z-lethal and sex-limited in the egg stage with a simple genetic system of high-tech with fine silk features. In the experiment, sex-limited C-8ngl breed of Bombyx mori L. mulberry silkworm in the egg stage and balanced on embryonic Z-lethal, also sex-limited trw2w2 × L-67 line, as well as non-sex-limited simple L-28 line, were used. In the second stage of improvement, an analyzer crossing was performed using translocation lines sex-limited in the egg stage to obtain information on which of the double lethal was present in the obtained F1, F2, F3 аnd F4 generation genotype. Genetic schemes have been developed to monitor ℓ1 and ℓ2 embryonic lethal attached to the Z chromosome in F1, F2, F3 аnd F4 generations obtained by backcrossing and to show the extent to which they are present in each generation.

​​Evaluation of Cluster Bean [Cyamopsis tetragonoloba (L.) Taub] Genotypes for Drought Stress Adaptation and its Effects on Yield

Background: Cluster bean is mostly grown in dry land arid zone areas for various purposes as vegetable, seed, fodder and other industrial uses because of its gum presence in endosperm. Methods: An experiment was conducted under the rain out shelter for the evaluation of drought adaptability of selected 10 genotypes of cluster bean. The physiological parameters were used to screen the drought resistance and also recorded various yield and yield attributing parameters at the time of harvesting. Result: Among the genotypes, Pusa Navbahar was observed well adaptability having adequate relative water content, maximum chlorophyll content, stomata per unit area and higher dry matter accumulation followed by genotype IC116866. Furthermore, yield and yield attributing parameters also showed significant differences; Pusa Navbahar was recorded maximum plant height (188.6 cm), leaves per plant (173.9), pods per plant (123.9), pod length (7.1 cm) and test weight (14.3 g) and well adaptability of primary and secondary root with deep in nature under the drought stress among the genotypes. Therefore, this study would be very helpful in the proper selection of genotypes as a source of drought resistance lines in future breeding and crop improvement programmes.

Overexpression of Modified CENH3 in Maize Stock6-Derived Inducer Lines Can Effectively Improve Maternal Haploid Induction Rates.

Maize (Zea mays) doubled haploid (DH) breeding is a technology that can efficiently generate inbred lines with homozygous genetic backgrounds. Haploids are usually produced through in vivo induction by haploid inducer lines in maize. Currently, two approaches are usually used to develop maize haploid inducer lines. One is through the conventional breeding improvement based on the Stock6 germplasm, and this strategy is extensively used to induce maternal haploids in commercial maize DH breeding. Another strategy, newly developed but less utilized so far, is by genetic manipulation of the Centromeric Histone3 (CENH3) in regular lines. However, whether both approaches can be combined to develop the haploid inducer line with higher maternal haploid induction rate (HIR) has not been reported. In this study, we manipulated the Stock6-derived inducer lines by overexpressing maize CENH3 fused with different fluorescent protein tags and found that the engineered Stock6-derived lines showed an obvious increase in the maternal HIR. Intriguingly, this above strategy could be further improved by substituting a tail-altered CENH3 for the full-length CENH3 in the tagged expression cassette, resulting in a maternal HIR up to 16.3% that was increased by ~6.1% than Stock6-derived lines control. These results suggested that integration of two in vivo haploid induction methods could rapidly and effectively improve the maternal HIRs of maize Stock6-derived inducer lines, and provided a potentially feasible solution for further optimizing the process of commercial maize DH breeding.

Progenitor species hold untapped diversity for potential climate-responsive traits for use in wheat breeding and crop improvement.

Climate change will have numerous impacts on crop production worldwide necessitating a broadening of the germplasm base required to source and incorporate novel traits. Major variation exists in crop progenitor species for seasonal adaptation, photosynthetic characteristics, and root system architecture. Wheat is crucial for securing future food and nutrition security and its evolutionary history and progenitor diversity offer opportunities to mine favourable functional variation in the primary gene pool. Here we provide a review of the status of characterisation of wheat progenitor variation and the potential to use this knowledge to inform the use of variation in other cereal crops. Although significant knowledge of progenitor variation has been generated, we make recommendations for further work required to systematically characterise underlying genetics and physiological mechanisms and propose steps for effective use in breeding. This will enable targeted exploitation of useful variation, supported by the growing portfolio of genomics and accelerated breeding approaches. The knowledge and approaches generated are also likely to be useful across wider crop improvement.

Emerging Strategies Mold Plasticity of Vegetable Plants in Response to High Temperature Stress.

As a result of energy consumption and human activities, a large amount of carbon dioxide emissions has led to global warming, which seriously affects the growth and development of plants. Vegetables are an indispensable part of people’s diet. In the plant kingdom, a variety of vegetables are highly sensitive to climate change. For them, an increase of just a few degrees above their optimum temperature threshold can result in a loss of yield and quality. Emerging strategies such as practice management and breeding varieties in response to above-optimal temperatures are critical for abiotic stress resistance of vegetable crops. In this study, the function and application of multiple strategies, including breeding improvement, epigenetic modification directed generation of alleles, gene editing techniques, and accumulation of mutations in multigenerational adaptation to abiotic stress, were discussed in vegetable crops. It is believed to be meaningful for plants to build plasticity under high temperature stress, thus generating more genetic structures for heat resistant traits in vegetable products.

English

Yam anthracnose disease (YAD), caused by the fungus Colletotrichum gloeosporioides Penz, is the most damaging fungal disease of Dioscorea alata yam worldwide. Local yam varieties, which sustain Côte d'Ivoire’s farmers and other end-users livelihoods, are highly susceptible to this pathogen. Thus, there is a need for developing new yam cultivars to sustain yam production in Côte d'Ivoire. To achieve such objective, identifying and selecting sources of resistance within the existing germplasm is crucial prior to the establishment of a breeding program. This study, therefore, aimed at determining the field resistance to C. gloeosporioides of 115 D. alata landrace varieties. Field experiments were conducted at the Research Station for Food Crops (SRCV) of the CNRA, Bouaké City, in Central Côte d'Ivoire, for three growing seasons. Results showed that symptoms of the anthracnose disease were more noticeable four months after planting (P3): high disease severity and incidence scores. At this period, ‘Betebete’ group (DSS = 3.40 and DI = 99.81%) was the most sensitive to anthracnose disease across years. In contrast, ‘Brazo’ (DSS = 2.24 and DI = 94.81%) and ‘Florido’ (DSS = 2.59 and DI = 97.23%) groups were the least sensitive. This finding indicates that local yam accessions from Côte d’Ivoire have different sensitivity levels to anthracnose disease attacks. Therefore, the genetic diversity from this work should be further exploited by yam breeding and genetic improvement programs for developing cultivars, combining resistance to YAD, high yield potential, and superior tuber quality to meet producers and consumers’ needs. Key words: Anthracnose, Côte d'Ivoire, disease resistance, environment, Dioscorea alata, plant breeding.

Apple cultivars and rootstocks assay for the identification of diverse viruses and healthy genotypes for breeding

The prevalence of harmful viruses, viz., apple stem grooving virus (ASGV), apple stem pitting virus (ASPV), apple chlorotic leaf spot virus (ACLSV), apple mosaic virus (ApMV), and tomato ringspot virus (ToRSV) in apple tree plantations in the Ryazan, Yaroslavl, and Moscow regions, Russian Federation, based on genotype features, planting type (industrial, collection, and repository), and tree age was studied during 2018–2021. The prevalence of harmful and latent viruses ranged from 49.6% to 53.8% in apple cultivars and from 8.3% to 100% in apple clonal rootstocks. The most common virus in the Moscow and Yaroslavl regions was ACLSV (34.7% and 53.8%) and that in the Ryazan region was ApMV (33.3%). Relative to that in young apple trees, the virus influence in older tree tissues was higher by 20% to 43% depending on virus type. Monoviral infection prevailed (59% of all trees were infected with one virus) in the studied apple tree cultivars. Of the cultivars, 25% were infected by a complex of two viruses (ASPV + ACLSV), 10% were infected by three viruses, and 6% were infected by four viruses. The highest prevalence of latent viruses was observed in old Russian cultivars (53.5%) and selections from old foreign cultivars (57.2%). Virus occurrence was slightly lower (51.6%) in new Russian cultivars than in other cultivars. Columnar apple tree cultivars had the lowest virus occurrence (30%) and were found to be more tolerant than other genotypes. The highest virus incidence was recorded in industrial orchards (63.4%), followed by that recorded in collection (20.8%) and repository (18.3%) plantations. By using ELISA, the apple genotypes that were free from harmful viruses were identified as source plants, i.e., 183 plants from 18 apple tree cultivars and 131 plants from clonal rootstocks. Results indicated that virus-free apple germplasm is highly effective for the successful implementation of breeding and genetic improvement.

Metabolome and whole transcriptome analyses reveal the molecular mechanisms underlying terpenoids biosynthesis in Sapindus mukorossi fruits

Sapindus mukorossi fruit has been widely used as a source of daily necessities, cosmetics, biomedicine, and biodiesel due to its high terpenoids content. However, a systematic inventory of the regulatory mechanisms of terpenoids biosynthesis at different stages of fruit growth is still lacking. Here, we identified 50 terpenoid metabolites by terpenoid-targeted metabolomics and found that the most abundant kinds of terpenoids are triterpenoids and sesquiterpenoids. Mukurozioside and pyishiauoside of sesquiterpenoids were significantly upregulated in the mature fruit (S3) compared with the young fruit (S1) and mid-mature fruit (S2), indicating that they may be important factors leading to a high content of terpenoids. A total of 1669 differentially expressed (dif) lncRNAs, 13 dif-circRNAs, 219 dif-miRNAs, and 17,529 dif-mRNAs were identified by whole-transcriptome data. Enrichment analysis showed that these dif-RNAs were significantly enriched in phenylpropanoid biosynthesis, metabolic process, and plant hormone signal transduction. Co-expression and ceRNA network analysis showed that lncRNA:MSTRG.18127.1 was positively correlated with gma-miR156k, SmHSF14, and SmAXY4, regulating secondary metabolite biosynthesis. Correlation analysis between transcriptome and metabolite profiling showed that SmSE, Smβ-AS, SmCYP716A, SmUGT73, SmUGT94, SmTPS1, and SmTPS26 are key regulatory genes and that the upregulation of these genes may be beneficial to terpenoids biosynthesis. These findings can help elucidate the molecular mechanisms and regulatory networks of terpenoids biosynthesis in S. mukorossi and provide a biological basis for genomics-enabled improvements in molecular breeding.

De Novo Assembly of 20 Chicken Genomes Reveals the Undetectable Phenomenon for Thousands of Core Genes on Microchromosomes and Subtelomeric Regions.

The gene numbers and evolutionary rates of birds were assumed to be much lower than those of mammals, which is in sharp contrast to the huge species number and morphological diversity of birds. It is, therefore, necessary to construct a complete avian genome and analyze its evolution. We constructed a chicken pan-genome from 20 de novo assembled genomes with high sequencing depth, and identified 1,335 protein-coding genes and 3,011 long noncoding RNAs not found in GRCg6a. The majority of these novel genes were detected across most individuals of the examined transcriptomes but were seldomly measured in each of the DNA sequencing data regardless of Illumina or PacBio technology. Furthermore, different from previous pan-genome models, most of these novel genes were overrepresented on chromosomal subtelomeric regions and microchromosomes, surrounded by extremely high proportions of tandem repeats, which strongly blocks DNA sequencing. These hidden genes were proved to be shared by all chicken genomes, included many housekeeping genes, and enriched in immune pathways. Comparative genomics revealed the novel genes had 3-fold elevated substitution rates than known ones, updating the knowledge about evolutionary rates in birds. Our study provides a framework for constructing a better chicken genome, which will contribute toward the understanding of avian evolution and the improvement of poultry breeding.

Development and Application of a High-Resolution Melting Analysis with Unlabeled Probes for the Screening of Short-Tailed Sheep TBXT Heterozygotes.

Simple SummaryTBXT (c.333G > C; c.334G > T) has been identified as a molecular genetic marker in short-tailed sheep. This paper describes a high-resolution melting (HRM) analysis using unlabeled probes and asymmetric PCR for the detection of genetic variants of TBXT in short-tailed sheep populations. The detection results of this method are consistent with those of Sanger sequencing and can help farmers with marker-assisted breeding.The short-tailed phenotype has long been considered one of the best traits for population genetic improvement in sheep breeding. In short-tailed sheep, not only is tail fat eliminated but also the pubic area is exposed due to the lack of a tail covering, giving them an advantage in reproduction. Recent studies have shown that two linked mutations in sheep TBXT at nucleotides 333 and 334 are associated with the short-tailed phenotype. In the population of short-tailed sheep, several heterozygous mutants of this gene are found. In our research, we used high-resolution melting (HRM) to identify homozygous and heterozygous genotypes in a flock of short-tailed sheep and compared the results with those of Sanger sequencing, which were identical. This demonstrates that our established HRM method, a rapid and inexpensive genotyping method, can be used to identify homozygous and heterozygous individuals in short-tailed sheep flocks.

Transcriptome Analysis Reveals a Gene Expression Pattern That Contributes to Sugarcane Bud Propagation Induced by Indole-3-Butyric Acid.

Sugarcane is a cash crop that plays an integral part in the sugar industry. The Sustainable Sugarcane Initiative (SSI) has been adopted globally, ensuring enough and aiming for more yield, helping increase disease-free sugarcane cultivation. Single-bud seeds could be the best approach for sugarcane cultivation. Indole-3-butyric acid (IBA) is a rooting agent utilized significantly in seedling propagation. Greenhouse experiment results discovered the significant growth promotion in sugarcane seedlings and accumulation of plant hormones at 100 ppm IBA. Next, we performed transcriptomic analysis of sugarcane buds using RNA sequencing and compared their gene expression during root development due to affect of IBA (100 ppm). A total of 113,475 unigenes were annotated with an average length of 836 bp (N50 = 1,536). The comparative RNA-seq study between the control (CK) and IBA-treated (T) buds showed significant differentially expressed unigenes (494 upregulated and 2086 downregulated). The IBA influenced major biological processes including metabolic process, the cellular process, and single-organism process. For cellular component category, cell, cell part, organelle, membrane, and organelle part were mainly affected. In addition, catalytic activity and binding were primarily affected in the molecular function categories. Furthermore, the expression of genes related to plant hormones and signaling pathways was analyzed by qRT-PCR, which was consistent with the RNA-seq expression profile. This study provides new insights into the IBA response to the bud sprouting in sugarcane based on RNA sequencing, and generated information could help further research on breeding improvement of sugarcane.