Genetic Improvement Research Articles

TRANSPARENT TESTA 16 collaborates with the MYB-bHLH-WD40 transcriptional complex to produce brown fiber cotton.

Naturally colored cotton (NCC; Gossypium spp.) does not require additional chemical dyeing and is an environmentally friendly textile material with great research potential and applications. Our previous study using linkage and association mapping identified TRANSPARENT TESTA 2 (Gh_TT2) as acting on the proanthocyanin synthesis pathway. However, limited information is available about the genetic regulatory network of NCC. Here, we verified the effectiveness of Gh_TT2 and the roles of Gh_TT2 and red foliated mutant gene (Re) in pigment formation and deposition of brown fiber cotton (BFC). Variations in Gh_TT2 derived from interspecific hybridization between Gossypium barbadense acc. Pima 90-53 and Gossypium hirsutum acc. Handan208 resulted in gene expression differences, thereby causing phenotypic variation. Additionally, the MYB-bHLH-WD complex was found to be negatively modulated by TRANSPARENT TESTA 16/ARABIDOPSIS BSISTER (TT16/ABS). RNA-seq suggested that differential expression of homologous genes of key enzymes in the proanthocyanin synthesis pathway strongly contributes to the color rendering of natural dark brown and light brown cotton. Our study proposes a regulatory model in BFC, which will provide theoretical guidance for the genetic improvement of NCC.

Characterization of the myostatin gene in the neotropical species Piaractus mesopotamicus and the possibility of its use in genetic improvement programs.

The myostatin gene has played an important role in the genetic improvement of the main species of economic importance; however, it has not yet been described for some Neotropical fish essential for aquaculture. This study aimed to characterize the myostatin gene of pacu, Piaractus mesopotamicus, and investigate the association of a microsatellite marker in this gene with the weight of fish. The myostatin gene sequence was obtained after following a RACE-PCR strategy based on a partial mRNA sequence available in the GenBank database and the alignment of myostatin sequences from other fish species. The obtained sequence for the P. mesopotamicus gene was analyzed for short tandem repeats, and one dinucleotide was observed at the 3´untranslated region. A short tandem repeat polymorphism was verified in a wild population. Subsequently, the STR was evaluated in a test population of 232 animals in two 220m² concrete tanks at the Aquaculture Center of Unesp. Eight alleles and 22 genotype combinations were identified. A significant association was observed between microsatellite marker polymorphisms and the weight traits (WEIGHT1 and WEIGHT2). Alleles 210, 222, 226, and 230 were found to favor weight gain. In summary, this study contributes to the characterization of the myostatin gene in pacu fish and identifies an association between a STR and weight traits. Thus, this gene could be used as a target for genetic breeding using molecular strategies such as CRISPR and quantitative strategies such as marker-assisted selection, which would contribute to improving the production of the species.

A Comprehensive Analysis of CSN1S2 I and II Transcripts Reveals Significant Genetic Diversity and Allele-Specific Exon Skipping in Ragusana and Amiatina Donkeys.

The αs2-casein is a phosphoprotein secreted in the milk of most mammals, and it is the most hydrophilic of all caseins. Contrary to genes found in ruminants, in donkeys two different encoding genes for donkey αs2-casein (CSN1S2 I and CSN1S2 II) have been identified. However, unlike in ruminants, the variability at these loci has not been characterized in detail in donkeys until now. In this study, we analyze the transcript profile of the donkey CSN1S2 I and CSN1S2 II genes, and we identify and describe the variability of these loci in the Ragusana and Amiatina breeds reared in Italy. The analysis of the CSN1S2 I Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR) products and subsequent sequencing showed, in addition to correctly spliced mRNA, seven other minor mRNAs resulting from differential splicing events involving, in various combinations, entire exons (4, 5, 6, and 11), parts of exons (5' or 3' end of exon 17), or the recognition of intronic sequences as an exon (exon 12'). Similarly, the transcription analysis of the CSN1S2 II gene revealed a remarkable variability in splicing events, mainly concerning the alternative insertion of an extra exon 7 (named 7'); the first 33 bp of exon 13; or the alternative skipping of exons 9, 10, 11, 12, and 15, and their combinations. At the mRNA level for CSN1S2 I, seven SNPs were observed, five of which led to amino acid changes: p.T73>A, p.I109>V, p.I130>V, p.I146>T, and p.D217>Y. Similarly, nine SNPs were observed at the CSN1S2 II locus, seven of which are non-synonymous: p.L63>F, p.H70>Q, p.D90>N, p.129A>T, p.H131>Y, p.E144>G, and p.F157>S. In addition, the DNA sequencing of exon 17 and flanking introns of the CSN1S2 I gene revealed a G>A transition at the splice acceptor site of CSN1S2 I exon 17 (FM946022.1:c.375-1G>A), resulting in an allele-specific skipping of the first 15 nucleotides of this exon, which encode the peptide 176NKINQ180, and the recognition of an in-frame cryptic splicing acceptor site: arAACAAAATCAACCAG. A genotyping method based on restriction fragment length polymorphism (XbaI PCR-RFLP) was set up for this SNP. In the total population studied (105 Ragusana and 14 Amiatina donkeys), the A allele had a frequency of 0.2437 with no evidence of deviation from the Hardy-Weinberg equilibrium. This study adds new knowledge regarding the genetic variability of αs2-caseins in donkeys and may contribute significantly to the genetic improvement of milk production for this species.

Exploring an economic and highly efficient genetic transformation and genome-editing system for radish through developmental regulators and visible reporter.

Radish (Raphanus sativus L.) is one of the most important root vegetable crops worldwide. However, gene function exploration and germplasm innovation still face tremendous challenges due to its extremely low transformation efficiency. Here, an economic and highly efficient genetic transformation method for radish was explored by Agrobacterium rhizogenes-mediated transformation with the help of combining special developmental regulator (DR) genes and the visual identification reporter. Firstly, the RUBY gene, a betalain biosynthesis system, could result in a visual red-violet color used as a convenient and effective reporter for monitoring transgenic hairy roots screening of radish. However, the hairy roots-to-shoots conversion system of radish still stands as a barrier to the obtainment of whole transgenic plants, although different hormone combinations and various culture conditions were tried. Following, two DR genes including Wuschel2 (Wus2) and isopentenyl transferase (ipt), as well as their combination Wus2-ipt were introduced for the shoot regeneration capacity improvement. The results showed that the transgenic shoots could be directly generated without externally supplying any hormones in the presence of a Wus2-ipt combination. Then, Wus2-ipt along with the RUBY reporter was employed to establish an efficient genetic transformation system of radish. Moreover, this system was applied in generating gene-edited radish plants and the phytoene desaturase (RsPDS) gene was effectively knockout through albino phenotype observation and sequencing analysis. These findings have the potential to be widely applied in genetic transformation and genome-editing genetic improvement of other vegetable species.

GWAS for root yield and its contributing traits in Withania somnifera (L.) dunal: First report

Ashwagandha [Withania somnifera (L.) Dunal] is a significant medicinal plant, with limited information on its genetic variability. This study evaluateed genetic diversity among 96 ashwagandha genotypes with the aim of developing strategies to improve root yield and secondary metabolites. A joint ANOVA indicated significant variability within the evaluated panel. Key traits, such as root girth, fresh root yield and dry root yield showed positive and significant correlations at both tested years. Molecular markers (SRAP, ISSR, and SSR) were used to assess genetic diversity. Amplified PCR products ranged from 210 bp (SRAP-22) to 1350 bp (SRAP-19), with PIC value ranged from 0.332 (SSR 20) to 0.494 (ISD 11), indicated moderate informativeness of markers. Genetic diversity analysis using Dice's coefficient formed six clusters, identifying two genotypes (86 and 87) as highly diverse. Population structure analysis revealed five clusters with an Fst range of 0.21–0.36, indicating allele flow among genotypes. The highest genetic differentiation was observed between clusters G2 and G4 (Fst = 0.1253). On the basis of structure analysis, genotypes in cluster G5 exhibited similar genetic make-up. A genome-wide association study (GWAS) identified a 490 bp locus of the SRAP 49 marker as highly effective and informatice. This locus was broadly associated with fresh root yield (FW) and dry root yield (DW) across individual and pooled environments. The positive correlation between these traits suggests simultaneous improvement is feasible. This study highlights the importance of genetic diversity for enhancing root yield and provides valuable insights for the genetic improvement of ashwagandha.

T2T genome assemblies of Fallopia multiflora (Heshouwu) and F. multiflora var. angulata

The traditional Chinese medicinal plant Fallopia multiflora (hereafter AYY) is well known for its anti-hyperlipidaemia, immunomodulating, and hepatoprotective effects, attributed to its abundance of anthraquinones and stilbene glycosides, which are distinct to its variety F. multiflora var. angulata (hereafter CYY) in proportion and composition. In this study, telomere-to-telomere (T2T) genomes were assembled for AYY and CYY using PacBio HiFi reads and Hi-C data. The genome sizes, percentages of repetitive sequences, and numbers of protein-coding genes of AYY and CYY assemblies were 1,458.37 Mb/70.48%/84,768 and 1,174.38 Mb/67.36%/69,100, respectively. Comprehensive assessments confirmed high continuity (contig N50: 112.58 Mb and 94.83 Mb; number of gaps: 9 and 5), completeness (BUSCOs: 97.30% and 97.60%; LAI: 16.93 and 16.77), and correctness (QV: 51.42 and 52.60) of AYY and CYY assemblies. These T2T genomes of F. multiflora provide valuable resources for studying the biosynthesis of specialized metabolites and facilitating precise genetic improvement.

The Azawak zebu bred at the Toukounous experimental centre in Niger: reproduction performance and estimation of genetic parameters.

The aim of this study was to estimate the genetic parameters of the reproductive performance of the Azawak zebu, bred on station during the period 1981 to 2007, in order to contribute to the implementation of an effective selection programme for improving the zootechnical performance of cattle herds. The data contained records of 2453 calvings from 650 Azawak cows, daughters of 55 bulls, all bred at the Toukounous experimental centre (Niger). Non-genetic factors were evaluated using linear mixed models and genetic parameters were estimated using REML procedures with a multi-trait animal model. The effects of year and calving rank were significant (P < 0.001) for the three reproductive traits studied. Heritability was low for age at first calving (h2 = 0.09 ± 0.03) and calf birth weight (h2 = 0.07 ± 0.03). It was moderate for calving interval (h2 = 0.30 ± 0.04) indicating the possibility of genetic improvement of this trait by selection. Repeatability estimates for calf birth weight and calving interval were 0.10 ± 0.02 and 0.42 ± 0.03 respectively. Calving interval had very strong and significant genetic correlations with age at first calving (0.84 ± 0.08) and calf birth weight (-0.40 ± 0.20). There was also a significantly favourable genetic correlation between calf weight at birth and age at first calving (-0.32 ± 0.25), implying a simultaneous improvement in all three reproductive traits through selection. An increase in heritability of calf birth weight was observed after the active phase of the program, reflecting an overly open selection scheme. These genetic parameter estimates suggest that the three reproductive traits could be used in selection index with the aim to improve the three reproductive traits of Azawak cattle.

The roles of Magnaporthe oryzae avirulence effectors involved in blast resistance/susceptibility.

Phytopathogens represent an ongoing threat to crop production and a significant impediment to global food security. During the infection process, these pathogens spatiotemporally deploy a large array of effectors to sabotage host defense machinery and/or manipulate cellular pathways, thereby facilitating colonization and infection. However, besides their pivotal roles in pathogenesis, certain effectors, known as avirulence (AVR) effectors, can be directly or indirectly perceived by plant resistance (R) proteins, leading to race-specific resistance. An in-depth understanding of the intricate AVR-R interactions is instrumental for genetic improvement of crops and safeguarding them from diseases. Magnaporthe oryzae (M. oryzae), the causative agent of rice blast disease, is an exceptionally virulent and devastating fungal pathogen that induces blast disease on over 50 monocot plant species, including economically important crops. Rice-M. oryzae pathosystem serves as a prime model for functional dissection of AVR effectors and their interactions with R proteins and other target proteins in rice due to its scientific advantages and economic importance. Significant progress has been made in elucidating the potential roles of AVR effectors in the interaction between rice and M. oryzae over the past two decades. This review comprehensively discusses recent advancements in the field of M. oryzae AVR effectors, with a specific focus on their multifaceted roles through interactions with corresponding R/target proteins in rice during infection. Furthermore, we deliberated on the emerging strategies for engineering R proteins by leveraging the structural insights gained from M. oryzae AVR effectors.

Transcriptome analysis reveals the dynamics of gene expression during early embryonic development of hybrid groupers

Distant hybridization is widely applied in genetic improvement of aquatic animals. Although this technique should be suitable for genetic improvement of grouper, few studies related to offspring produced via distant hybridization have been reported. There we studied the gene expression dynamics of early embryonic development of groupers from self-breeding, intraspecific breeding and intergeneric hybridization. We first obtained offspring from female brown-marbled grouper (Epinephelus fuscoguttatus) and male leopard coral grouper (Plectropomus leopardus) and described the morphological characteristics of different developmental stages of embryos. We then constructed the transcriptome maps during early embryonic development of hybrid groupers. In addition, we also found that the process of MZT occurred from high blastula to early gastrula stage in the embryo of hybrid grouper and that wnt signaling pathway play an important role in dorsal-ventral axial formation during embryonic development of grouper. These results provide a foundation for the hybrid breeding of leopard coral grouper.

Recovery of Novel Sequence Variants in Chemically Mutagenized Seed and Vegetatively Propagated Coffea arabica L.

The negative effects of climate change impact both farmers and consumers. This is exemplified in coffee, one of the most widely consumed beverages in the world. Yield loss in high-quality Coffea arabica L., due to the spread of coffee leaf rust (Hemileia vastatrix), results in lower income for subsistence farmers and volatile prices in markets and cafes. Genetic improvement of crops is a proven approach to support sustainable production while mitigating the effects of biotic and abiotic stresses and simultaneously maintaining or improving quality. However, the improvement of many species, including coffee, is hindered by low genetic diversity. This can be overcome by inducing novel genetic variation via treatment of seeds or cells with mutagens. To evaluate this approach in coffee, mutant populations created by incubating seed or embryogenic calli with the chemical mutagens ethyl methanesulphonate or sodium azide were subject to reduced-representation DNA sequencing using the ddRADseq approach. More than 10,000 novel variants were recovered. Functional analysis revealed hundreds of sequence changes predicted to be deleterious for gene function. We discuss the challenges of unambiguously assigning these variants as being caused by the mutagenic treatment and describe purpose-built computational tools to facilitate the recovery of novel genetic variation from mutant plant populations.

CRISPR-Cas9: Unraveling Genetic Secrets to Enhance Floral and Fruit Traits in Tomato.

Tomato, a globally consumed vegetable, possesses vast genetic diversity, making it suitable for genetic manipulation using various genetic improvement techniques. Tomatoes are grown extensively for their market value and health benefits, primarily contributed by enhanced yield and nutritional value respectively, influenced by floral and fruit traits. Floral morphology is maintained by genes involved in meristem size control, regulation of inflorescence transition, and pollen development. SP (SELF-PRUNING) and SP5G (SELF-PRUNING 5G) determine growth habit and flowering time. RIN (RIPENING INHIBITOR) and PG (POLYGALACTURONASE) are responsible for the shelf life of fruits. In addition to this, nutrition-enriched tomatoes have been developed in recent times. In this review, we comprehensively discuss the major genes influencing floral morphology, flowering time, fruit size, fruit shape, shelf life, and nutritional value, ultimately resulting in enhanced yield. Additionally, we address the advances in CRISPR/Cas9 applied for the genetic improvement of tomatoes along with prospects of areas in which research development in terms of tomato genetic improvement has to be advanced.

Genetic Diversity Analysis and Fingerprint Construction for 87 Passionfruit (Passiflora spp.) Germplasm Accessions on the Basis of SSR Fluorescence Markers

A comprehensive genetic diversity analysis of 87 Passiflora germplasm accessions domesticated and cultivated for several years in the karst region of Guizhou, China, was conducted utilizing simple sequence repeat (SSR) fluorescent markers. These Passiflora species, renowned for their culinary and medicinal value, could bring significant economic and ecological benefits to the region. This study aimed to assess the genetic resources of these species and facilitate the selection of superior cultivars adapted to the karst environment. Our analysis revealed an abundance of SSR loci within the Passiflora transcriptome, with single-base repeats being the most prevalent type. Through rigorous primer screening and amplification, we successfully identified 27 SSR primer pairs exhibiting robust polymorphisms. Further interrogation at eight microsatellite loci revealed 68 alleles, underscoring the high level of genetic diversity present in the cultivated accessions. The average expected heterozygosity was 0.202, with the ssr18 locus exhibiting the highest value of 0.768, indicating significant genetic variation. The mean polymorphic information content (PIC) of 0.657 indicates the informativeness of these SSR markers. Comparative analyses of the cultivated and potential wild progenitors revealed distinct genetic variations among the different Passiflora types. Genetic structure and clustering analyses of the 87 accessions revealed seven distinct groups, suggesting gene flow and similarities among the resources. Notably, a DNA fingerprinting system was established using eight SSR primer pairs, effectively distinguishing the selected cultivars that had adapted to the karst mountainous region. This study not only deepens our understanding of Passiflora genetic resources in the karst environment but also provides a valuable reference for conservation, genetic improvement, and cultivar selection. The rich genetic diversity of the Passiflora germplasm underscores their potential for sustainable utilization in breeding programs aimed at enhancing the economic and ecological viability of these valuable plant species.

Fibre Medullation Characteristics in Peruvian Llamas (Lama glama)

Background: The textile use of llama fiber, achieved through genetic improvement, llama selection and management, shows great potential for producing high-quality clothing and fabrics; providing an alternative income to highland residents who raise llamas. The aim of this research was to determine the fiber medullation of white Ch´aku and Q´ara color varieties of Llamas (Lama glama) from the communities of the Macusani district, Puno Peru. Methods: A total of 88 Llamas from the Ch´aku and Q´ara white color varieties, including males and females, from the age of milk teeth and two teeth, were used. Fiber samples of approximately 10 g were taken from the thigh, middle rib and shoulder, totaling 264 samples. Samples were analyzed at the Fiber Laboratory of the District Municipality of Corani, using the FIBER MED equipment. Data were analyzed in a completely randomized design (CRD) with a 2(variety) × 2 (sex) × 2 (age group) × 3 (body area) factorial arrangement. Result: The percentage of fiber medullation types in Ch´aku and Q´ara Llamas averaged 46.02% and 47.38%, showing no significant difference (p greater than 0.05). In Ch´aku Llamas, a statistical difference was observed by sex (p less than 0.05) for the percentage of medullated, non-medullated and continuous fibers in males and females. In Q´ara variety, there was a significant difference in the percentage of medullated, non-medullated and continuous fibers between milk teeth and two teeth age groups. There was no significant difference (p greater than 0.05) between body area samples.

Mutation profiling through whole genome sequencing of electron beam-induced black gram (Vigna mungo L. Hepper) mutant

Purpose Black gram (Vigna mungo [L.] Hepper) is an important annual legume with great economic, nutritional and ecological significance. Novel variations through induced mutagenesis can accelerate narrow genetic base-impeded black gram improvement. This is a first study on characterization of genome-wide mutation spectrum induced by electron beam (EB). Materials and methods Black gram genotype ‘Pant U-31’ was irradiated with 400 Gy EB generated in a 10 MeV LINAC. A stable mutant PM-32 (M6) was re-sequenced by combining Illumina (BIOO Scientific, Inc., Austin, TX) and Nanopore Technologies (Oxford, UK). Variants were predicted in reference to the available whole genome scaffold level draft assembly of parent ‘Pant U-31’. Results Genome analysis predicted a total of 76,893 genes of which 58,517 were annotated. The identified variants totaling 728,161, largely comprised (91.56%) of single base substitutions (SBSs) with a transition (Ti) to transversion (Tv) ratio of 1.95. Of the indels constituting 8.44% of total induced variants, insertions accounted for 4.29%, with preponderance of multiple bases (53.63%) and 2–5 bp insertions as the major class (33.71%). Multiple-base deletions (2–5 bases) formed the bulk (31.14%) of the total deletions. The genic variants (2438) with estimated high and moderate effects were located within 1271 predicted genes. A higher number of mutations were observed on chromosomes Vm1 (588) and Vm3 (428) with the highest frequency on chromosome Vm3 (every 0.07 Mb). Conclusions Our study reiterated the mutagenic utility of EB for inducing SBSs and small indels genome-wide. The knowledge gained from SNP-level profiling of EB-induced mutations can expedite comparative mutation breeding studies in legumes.

Full-Length Transcriptome Analysis and Characterization of DFRs Involved in the Formation of Anthocyanin in Allium wallichii

Allium wallichii is famous for its reddish-purple flowers, which can be utilized as cut flowers and garden landscaping. Flower color is mainly determined by flavonoids, betalains, carotenoids, as well as other pigments. However, there is no research on the color formation mechanism in A. wallichii, which restricts its genetic improvement and development of superior varieties. The flower of A. wallichii was collected for full-length transcriptome sequencing and metabolome analysis using PacBio SMART and UPLC-MS, respectively. A total of 45 anthocyanins were detected in its flower, and 75,778 transcripts of 107,208 non-redundant transcripts were annotated. Then, two AwDFRs were cloned and characterized using bioinformatics tools. Enzyme activity assays revealed that both AwDFR1 and AwDFR2 possessed DFR activity in vitro that only accepted DHQ and DHM as substrates, except for DHK. Finally, physiological results showed that AwDFR1 and AwDFR2 could restore the lacking phenotypes of Arabidopsis tt3 mutant and increase the content of anthoycanin in tobacco petals. The anthocyanins and transcriptome in A. wallichii were firstly reported, and AwDFR1 and AwDFR2 are key enzymes participating in the biosynthesis of anthocyanins. This research provides important guidance for future key gene mining, color improvement, and horticultural breeding in A. wallichii.

Quality diversity of three calcium-rich Primulina vegetables: A comprehensive analysis of calcium content, metabolite profiles, taste characteristics, and medicinal potential

Primulina plants native to karst regions are exceptionally rich in calcium and have been developed into high‑calcium leafy vegetables. However, limited knowledge of their metabolites, taste characteristics, and potential medicinal value restricts further genetic improvements. This study conducted a comprehensive analysis on three breeding species of Primulina vegetables. Common garden experiment demonstrated significant calcium enrichment capability, with calcium content ranging from 204.45 to 391.52 mg/100 g. Through widely-targeted metabolomics, 1121 metabolites were identified within these Primulina vegetables. Furthermore, comparative analysis identified 976 differentially accumulated metabolites across nine comparison groups, driven mainly by flavonoids, phenolic acids, and lipids. Integration of electronic tongue analysis and metabolomics revealed taste profiles and identified 17 key candidate compounds related to taste. Based on network pharmacology analysis, 32 active ingredients were found in Primulina vegetables, which highlighted potential medicinal value. These findings provide a data-driven foundation for breeding programs aimed at enhancing nutritional and flavor traits.

Genome-Wide Characterization and Development of Simple Sequence Repeat Markers for Molecular Diversity Analyses in Yellowhorn (Xanthoceras sorbifolium Bunge).

Yellowhorn (Xanthoceras sorbifolium Bunge) is a valuable ornamental, medicinal, and woody oilseed species that is indigenous to China. The breeding improvement of yellowhorn has been hindered by a lack of suitable markers and sufficient information regarding the molecular diversity of this species. In this study, we conducted a comprehensive analysis of the yellowhorn genome to characterize the simple sequence repeat (SSR) loci. A total of 4,007,201 SSRs were successfully identified. Among these markers, mono-nucleotide SSRs were most abundant in the genome, while the tri-nucleotide SSRs accounted for the highest proportion in coding sequences. The GO and KEGG function enrichment analysis revealed that most SSR loci in coding sequences were associated with potential biological functions. Additionally, we used 30 pairs of primers to amplify SSR markers to gain a better understanding of the genetic variation in yellowhorn germplasms. The average values of observed heterozygosity and polymorphism information content were 0.625 and 0.517, respectively. Population structure, phylogeny and principal component analyses identified two distinct subclusters. Furthermore, yellowhorn germplasms with the same geographical distribution tended to group together. Moreover, a total of 26 yellowhorn core collections, which accounted for approximately 14.94% of the total yellowhorn germplasms, effectively represented the genetic diversity of all original germplasms. Our findings not only unveiled the genetic diversity and population structure of yellowhorn germplasms but also investigated the yellowhorn core collection, which will serve as a strong basis for yellowhorn management and genetic improvement.

Screening and Site Adaptability Evaluation of Qi-Nan Clones (Aquilaria sinensis) in Southern China

In recent years, plantations of Aquilaria sinensis in China have been dominated by Qi-nan, yet there remains limited research on the growth evaluation and breeding of these clones. In this study, a multi-point joint variance analysis, an additive main effect and multiplicative interaction (AMMI) model, a weighted average of absolute scores (WAASB) stability index, and a genotype main effect plus a genotype-by-environment interaction (GGE) biplot were used to comprehensively analyze the yield, stability, and suitable environment of 25 3-year-old Qi-Nan clones from five sites in southern China. The results showed that all the growth traits exhibited significant differences in the clones, test sites, and interactions between the clones and test sites. The phenotypic variation coefficient (PCV) and genetic variation coefficient (GCV) of the clones’ growth traits at the different sites ranged from 16.56% to 32.09% and 5.24% to 27.06%, respectively, showing moderate variation. The medium–high repeatability (R) of tree height and ground diameter ranged from 0.50 to 0.96 and 0.69 to 0.98, respectively. Among the clones, Clones G04, G05, G10, G11 and G13 showed good growth performance and could be good candidates for breeding. Environmental effects were found to be the primary source of variation, with temperature and light primarily affecting growth, while rainfall influenced survival and preservation rates. Yangjiang (YJ) was found to be the most suitable experimental site for screening high-yield and stable clones across the different sites, whereas the tree height and ground diameter at the Chengmai (CM) site were significantly higher than at the other sites, and the Pingxiang (PX) and Zhangzhou (ZZ) sites showed poor growth performance. The findings suggest that Qi-nan clones are suitable for planting in southern China. There were also abundant genetic variations in germplasm resources for the Qi-nan clones. The five selected clones could be suitable for extensive planting. Therefore, large-scale testing is necessary for determining genetic improvements in Qi-nan clones, which will be conducive to the precise localization of their promotion areas.

Analysis of genetic diversity and genetic structure of indigenous chicken populations in Guizhou province based on genome-wide single nucleotide polymorphism markers

Guizhou province in China is rich in indigenous chicken breeds, playing an essential role in the genetic improvement of modern chickens. Genetic diversity has decreased in recent decades due to accelerated breeding processes and changing conservation priorities. To determine the genetic diversity and population structure of Guizhou indigenous chicken breeds, we used 55K genotyping arrays to conduct population genetic analysis on 233 individuals from 8 Guizhou indigenous breeds and 263 individuals from 9 Guizhou indigenous chicken populations. We evaluated the genetic diversity parameter (heterozygosity, proportion of polymorphic markers, and nucleotide diversity), linkage disequilibrium (LD), population structure, and genetic differentiation (FST and genetics distance). Genetic diversity results indicated that the genetic diversity of chicken breeds in Guizhou province is relatively affluent. Among Guizhou breeds, Baiyi black-bone and Guizhou yellow chicken displayed the lowest genetic diversity, as the 2 breeds exhibit lower PN and heterozygosity, the extent of linkage disequilibrium is higher. According to the LD pattern, Guizhou indigenous breeds can be divided into 3 categories. Population structure analysis showed a certain degree of genetic differentiation among local chickens in Guizhou. We argue that Chishui black-bone and Puan black-bone chickens are 2 different geographical regional groups of the same breed. In principal component analysis, individuals from the 2 groups clustered together, and the phylogenetic tree results showed that the 2 groups clustered together to form a branch independent of other breeds, and they displayed an identical pattern of ancestral lineage composition. The research results will provide a reference for protecting local chicken genetic resources in Guizhou Province and promote the protection and utilization of genetic resources.

Proteomic analysis of storage proteins in Phaseolus vulgaris associated with resistance to water stress

The common bean (Phaseolus vulgaris), a widely consumed legume in Ecuador, boasts low economic value, significant nutritional contributions, and a remarkable capacity to enhance soil fertility. Despite these attributes, its field productivity often needs to improve, with the water deficit emerging as a primary hindrance. Consequently, genetic enhancements have been incorporated into select varieties, conferring tolerance to specific levels of water scarcity stress. This study aimed to elucidate the distinctions in protein expression patterns responding to water deficiency stress across nine bean varieties. Protein patterns were scrutinized through two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), and selected protein spots were subjected to mass spectrometry analysis (MALDI-TOF MS/RP-LC-MS/MS). A comprehensive identification of 111 proteins was achieved and categorized based on their respective functions. Noteworthy among these were the desiccation-protectant protein (LEA14) and Desiccation-related protein PCC13–62, identified as proteins associated with the response to abiotic stress, particularly prevalent in the INIAP_473 cultivar. These findings underscore the potential for targeted genetic improvements to mitigate the impact of water deficit stress on common bean cultivation, contributing to enhanced agricultural resilience and productivity.