Breeding Programs Research Articles

Association mapping of mesocotyl and coleoptile length in rice using various genome‐wide association study models

AbstractThe mechanized direct seeding of rice (Oryza sativa L.) is a major trend nowadays. The elongation of rice mesocotyl and coleoptile can facilitate the rapid emergence of seedlings under deep mechanized sowing. Currently, most of the cultivated rice accessions have short mesocotyls or coleoptiles, with only a few related genes cloned. However, understanding and enhancing the ability of rice seedlings to rapidly emerge from deep sowing depths is crucial. Herein, we assessed 745 core rice germplasm accessions sown under a soil cover depth of 10 cm and found few long mesocotyl and coleoptile germplasms. We conducted genome‐wide association study using six models to obtain three or more multi‐model co‐localization candidate regions and calculated Fst between the phenotypes of extreme samples to determine genetic differences. The candidate regions associated with mesocotyl and coleoptile lengths were identified by integrating Fst and multi‐model localization results. This multi‐model localization method may accelerate the mining of genes related to the mesocotyl and coleoptile, providing valuable targets for functional validation and marker‐assisted selection in rice breeding programs.

Molecular analysis of St. Augustinegrass cultivar mixtures composition over time and latitude

AbstractSt. Augustinegrass [Stenotaphrum secundatum (Walt.) Kuntze] is commonly planted in residential and commercial landscapes as a cultivar monoculture predisposing this lawn to pest invasion and high‐maintenance inputs. Researchers have suggested that increasing genetic diversity by growing cultivars in mixtures may increase turfgrass stress resilience. However, the stability and uniformity of those mixtures has not been studied. The present study was carried out to evaluate the stability of St. Augustinegrass cultivars mixtures over time and across three latitudes. The study was conducted in Citra and Fort Lauderdale, FL, and Jackson Springs, NC. Simple‐sequence repeats markers were used to genotype leaf samples of St. Augustinegrass cultivars planted in two‐ and four‐cultivar mixtures. Leaf samples were collected 1 and 3 years after establishment. In all locations, cultivar richness and evenness declined over time. Similarly, the relative abundance of the least persistent cultivars decreased approximately 50%–100% depending on cultivar and location. Differences in growth patterns among cultivars resulted in cultivar displacement and the predominance of a single cultivar. Cultivars that covered the ground faster or formed dense canopies early after establishment were dominant at the end of the study. Locally developed cultivars tended to be more dominant in their original latitude. The use of cultivar mixtures may help the identification of vigorous, competitive, and stress tolerant cultivars in turfgrass breeding programs. However, their commercial use remains challenging as if the patterns observed here for 3 years are representative of a continuous trend, and they do not persist over time.

Plant Morphological and Leaf Anatomical Traits in Coffea arabica L. Cultivars Cropped in Gorongosa Mountain, Mozambique

Studies on the genetic diversity of coffee trees are important, considering their role in the maximization of productivity and quality. However, the success of a breeding program depends on the existence of genetic variability in the population under study. Our study aimed to evaluate the genetic diversity of the morpho-agronomic and anatomical leaf traits of different cultivars of Coffea arabica grown in the Gorongosa mountain region, in the area of Gorongosa National Park, Mozambique. The experiment assessed nine coffee cultivars based on their morpho-agronomic and anatomical traits. The plagiotropic branch diameter, leaf dry mass, leaf mass per area, number of epidermal cells + stomata, and stomatal form indicated differences among the studied cultivars. Among the nine C. arabica cultivars grown in the mountainous region of Gorongosa National Park, Mozambique, low genetic variability in morpho-agronomic traits was detected, while the genetic variability in leaf anatomical traits was higher. The nine cultivars were segregated into two groups, one consisting of Catucaí Amarelo 2SL and Catuaí Vermelho IAC 81, and the second consisting of Catuaí Amarelo IAC 39, Catucaí Vermelho 19/8, Acauã, Catucaí 785-15, Costa Rica, Catimor 128, and Catuaí Vermelho IAC 44. The cultivar segregation into the two groups indicated that the morpho-anatomical traits can be considered during the selection stages in breeding programs.

Development of Yein-Early, a Unique Fruit-Color and Leaf-Shape Mutant of Citrus unshiu, and Its Specific Selection Marker.

Citrus unshiu Marc. cv. Miyagawa-wase is one of the most widely cultivated citrus varieties on Jeju Island in Republic of Korea. Mutation breeding is a useful tool for inducing genetic diversity by causing genomic mutations in a short period of time. We previously conducted mutation breeding using gamma irradiation to develop new varieties of C. unshiu. Here, we describe one of these varieties, Yein-early, which has a redder peel, greater hardness, and higher sugar content compared with the wild type (WT). Yein-early leaves also showed a unique phenotype compared with the WT, characterized by longer longitudinal length, shorter transverse length, stronger curling, and longer petiole length. Genome resequencing of Yein-early and the WT uncovered significant single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels). These variations were crucial in identifying molecular markers unique to Yein-early. In addition, we developed an allele-specific PCR marker specifically targeting a homozygous SNP in Yein-early that distinguishes it from the WT and other citrus varieties. This study contributes to the understanding of pigment synthesis in fruits and provides a valuable tool for selection of the novel Yein-early variety in citrus breeding programs.

Genetic improvement and conservation of goats in tropic

Goats indeed have a significant historical and contemporary importance in human civilization, particularly in the realm of agriculture and food production. Their adaptability and widespread distribution have made them crucial for various societies across the world. Goats have played a central role in the Neolithic agricultural revolution, aiding in the spread of human civilization globally. Their adaptability allowed them to thrive in diverse environments, contributing to the sustenance and expansion of human settlements. Goats are highly adaptable and are found in a wide range of geographical regions. Their presence spans across continents, from tropical to temperate climates, showcasing their ability to thrive in various environmental conditions. There is diversity in the production performance of goats based on the region of the world and the specific breeds. Genetic improvement programs aim to enhance economically important traits such as milk production, growth rates and fiber production, thereby increasing productivity and income for goat farmers. Understanding the genetic parameters such as heritabilities and repeatabilities for various traits is crucial for designing effective breeding programs. These parameters provide insights into the genetic potential of goats for traits like milk production, growth and fiber quality. Heritability estimates for reproductive traits, body weight, daily gain and direct and maternal heritability are important for implementing selective breeding strategies aimed at improving overall productivity and efficiency in goat farming. Genetic improvement programs have been implemented in tropical environments to enhance milk production traits in goats. Genetic improvements have also targeted fiber production in goats, with a focus on traits such as grease fleece weight and average fiber diameter. These efforts aim to enhance the quality and quantity of fiber produced by goats for various commercial purposes. Despite the importance of conserving goat breeds with unique characteristics, planned conservation programs in tropical regions are often neglected. It’s emphasized that preserving indigenous goat breeds in their native habitats is essential for maintaining genetic diversity and ensuring future resilience in goat farming.

Combined Genome-Wide Association Studies (GWAS) and Linkage Mapping Identifies Genomic Regions Associated with Seedling Root System Architecture (RSA) under Different Nitrogen Conditions in Wheat (Triticum aestivum L.)

The nitrogen (N) use efficiency (NUE) in the roots of seedlings is beneficial for increasing crop yield. Creating marker-assisted selection for wheat root traits can assist wheat breeders in choosing robust roots to maximize nutrient uptake. Exploring and identifying the effect of different N supply conditions on root system architecture (RSA) is of great significance for breeding N efficient wheat varieties. In this study, a total of 243 wheat varieties native to the Yellow and Huai Valley regions of China were utilized for genome-wide association studies (GWAS). Furthermore, a recombinant inbred line (RIL) population of 123 lines derived from the cross between Avocet and Chilero was utilized for linkage examination. A hydroponic seedling experiment using a 96-well tray was conducted in the lab with two treatments: normal N (NN) and low N (LN). Five RSA traits, including the relative number of root tips (RNRT), relative total root length (RTRL), relative total root surface area (RTRS), relative total root volume (RTRV), and relative average root diameter (RARD), were investigated. GWAS and linkage analysis were performed by integrating data from the wheat 660 k single nucleotide polymorphism (SNP) chip and diversity arrays technology (DArT) to identify genetic loci associated with RSA. The results showed that, based on the ratio of RSA-related traits under two N supply conditions, a total of 497 SNP markers, which are significantly associated with RSA-related traits, were detected at 148 genetic loci by GWAS. A total of 10 QTL loci related to RSA were discovered and identified by linkage mapping. Combining two gene localization methods, three colocalized intervals were found: AX-95160997/QRtrl.haust-3D, AX-109592379/QRnrt.haust-5A, and AX-110924288/QRtrl.haust-7D/QRtrs.haust-7D. According to the physical location of the colocalization of these two sites, between 39.61 and 43.74 Mb, 649.97 and 661.55 Mb, and 592.44 and 605.36 Mb are called qRtrl-3D, qRnrt-5A, and qRtrl-7D. This study has the potential to enhance the effectiveness of selecting root traits in wheat breeding programs, offering valuable insights into the genetic underpinnings of NUE in wheat. These results could help in breeding wheat varieties with higher NUE by implementing focused breeding strategies.

Unraveling Promising Genetic Variability Associated with Strong Culm and Yield Parameters in Inter Sub-Specific Cross Derived Recombinant Inbred Lines in Rice (Oryza sativa L.)

Strengthening the rice culm through genetic improvement has been an important target in breeding to abate the lodging problem in rice. The present investigation was attempted to study the variability, genetic parameters and trait association in recombinant inbred lines (RILs) derived from inter sub-specific cross of elite indica mega variety ‘Swarna’ and Tropical japonica strong culm accession ‘IRGC 39111’. Analysis of Variance (ANOVA) displayed significant variation in RILs for all the traits studied. The investigation revealed high estimates of GCV and PCV along with high heritability and genetic advance as percent of mean (GAM) for all culm strength (CS) traits revealing the role of additive gene effect and selection of these traits shall be effective in rice improvement. Correlation studies revealed that the internode breaking weight (IBW) and bending moment at breaking(M) had a high significant positive correlation with all the CS traits, panicle weight and grain yield. Thus, the direct selection of positively associated traits can improve the lodging resistance in rice. The principal component analysis (PCA) showed that, seven principal components (PCs) out of 23 traits attributed approximately 92.9% of the total cumulative variability. The traits culm thickness (CT), Internode breaking weight (IBW), section modulus (SM), bending stress (BS), Bending moment at breaking (M) contributed maximum to the total diversity and the lines with higher trait values for the aforementioned traits could be utilized as donors to improve the culm strength and its attributing traits in future breeding programs. From this study, it is evident that tropical japonica lines can be a great source of genetic diversification for rice improvement.

Genetic Variation for Tolerance to High Temperatures in Tomato Using Critical Sterility Temperature

Tomato (Solanum lycopersicum L.) reproduction is influenced by temperature, prominently impacting yield. The ideal daytime range is between 25°C and 30°C and the nighttime temperature is around 20°C for tomato and deviations of a few degrees from these temperatures can have negative effects. The study assessed the effect of temperature on tomato pollen germination and aimed to ascertain the critical sterility temperature for pollen germination. In an open field, pollen from 10 genotypes (Anagha, Manuprabha, Vellayani Vijay, Akshaya, Nandi, IIHR26372, Pusa Rohini, Arka Saurabh, Arka Rakshak, and Arka Vikas) underwent In-vitro temperature exposure ranging from 32 to 40°C at 2°C intervals. Variations in In-vitro pollen germination percentage were observed across the genotypes, notably revealing a sharp decline after 36°C. This decline indicated a pivotal shift in pollen germination and viability. Genotypes, Anagha and Arka Saurabh, were identified as temperature tolerant and susceptible, respectively. The findings present an opportunity to incorporate temperature-dependent pollen response functions and identified genotypes into tomato breeding programs, offering significant implications for enhancing yield under varying temperature conditions.

Streamlining of Simple Sequence Repeat Data Mining Methodologies and Pipelines for Crop Scanning.

Genetic markers are powerful tools for understanding genetic diversity and the molecular basis of traits, ushering in a new era of molecular breeding in crops. Over the past 50 years, DNA markers have rapidly changed, moving from hybridization-based and second-generation-based to sequence-based markers. Simple sequence repeats (SSRs) are the ideal markers in plant breeding, and they have numerous desirable properties, including their repeatability, codominance, multi-allelic nature, and locus specificity. They can be generated from any species, which requires prior sequence knowledge. SSRs may serve as evolutionary tuning knobs, allowing for rapid identification and adaptation to new circumstances. The evaluations published thus far have mostly ignored SSR polymorphism and gene evolution due to a lack of data regarding the precise placements of SSRs on chromosomes. However, NGS technologies have made it possible to produce high-throughput SSRs for any species using massive volumes of genomic sequence data that can be generated fast and at a minimal cost. Though SNP markers are gradually replacing the erstwhile DNA marker systems, SSRs remain the markers of choice in orphan crops due to the lack of genomic resources at the reference level and their adaptability to resource-limited labor. Several bioinformatic approaches and tools have evolved to handle genomic sequences to identify SSRs and generate primers for genotyping applications in plant breeding projects. This paper includes the currently available methodologies for producing SSR markers, genomic resource databases, and computational tools/pipelines for SSR data mining and primer generation. This review aims to provide a 'one-stop shop' of information to help each new user carefully select tools for identifying and utilizing SSRs in genetic research and breeding programs.

Nutritional Qualities, Metabolite Contents, and Antioxidant Capacities of Yardlong Beans (Vigna unguiculata subsp. sesquipedalis) of Different Pod and Seed Colors.

Studying the effects of genetic and environmental factors on plant biochemical components helps in selecting the best varieties for the food industry and breeding programs. This study analyzed the nutritional qualities, secondary metabolites, and antioxidant activities of 14 field-grown yardlong beans accessions and how they are affected by differences in pod and seed colors. The analyzed parameters varied significantly among the yardlong bean accessions, with variances ranging from 1.36% in total unsaturated fatty acid content to 51.01% in DPPH• scavenging activity. Accessions YLB4, YLB7, and YLB14 performed the best, showing antioxidant indices of 100.00, 70.10, and 67.88%, respectively. Among these, YLB14 showed a characteristic property, having the highest levels of vitamin C (2.62 mg/g) and omega-6 to omega-3 ratio (2.67). It also had the second highest dietary fiber (21.45%), stearic acid (4.44%), and linoleic acid (40.39%) contents, as well as the lowest thrombogenicity index (0.38). Although cluster and principal component analyses did not clearly separate the yardlong beans based on pod or seed color, analysis of variance revealed that these factors and their interaction had significant effects on total phenol, DPPH• scavenging activity, ABTS•+ scavenging activity, and reducing power. In contrast, the nutritional parameters, except for dietary fiber, were not significantly affected by pod and seed color variations. Therefore, consuming yardlong beans of different pod and seed colors may not affect the overall nutrient intake. In general, this study identified yardlong beans with green pods and black seeds as good sources of antioxidants. Accordingly, further metabolomics and genomics studies are suggested to thoroughly explore their characteristics.

Integrating Hyperspectral Reflectance-Based Phenotyping and SSR Marker-Based Genotyping for Assessing the Salt Tolerance of Wheat Genotypes under Real Field Conditions.

Wheat breeding programs are currently focusing on using non-destructive and cost-effective hyperspectral sensing tools to expeditiously and accurately phenotype large collections of genotypes. This approach is expected to accelerate the development of the abiotic stress tolerance of genotypes in breeding programs. This study aimed to assess salt tolerance in wheat genotypes using non-destructive canopy spectral reflectance measurements as an alternative to direct laborious and time-consuming phenological selection criteria. Eight wheat genotypes and sixteen F8 RILs were tested under 150 mM NaCl in real field conditions for two years. Fourteen spectral reflectance indices (SRIs) were calculated from the spectral data, including vegetation SRIs and water SRIs. The effectiveness of these indices in assessing salt tolerance was compared with four morpho-physiological traits using genetic parameters, SSR markers, the Mantel test, hierarchical clustering heatmaps, stepwise multiple linear regression, and principal component analysis (PCA). The results showed significant differences (p ≤ 0.001) among RILs/cultivars for both traits and SRIs. The heritability, genetic gain, and genotypic and phenotypic coefficients of variability for most SRIs were comparable to those of measured traits. The SRIs effectively differentiated between salt-tolerant and sensitive genotypes and exhibited strong correlations with SSR markers (R2 = 0.56-0.89), similar to the measured traits and allelic data of 34 SSRs. A strong correlation (r = 0.27, p < 0.0001) was found between the similarity coefficients of SRIs and SSR data, which was higher than that between measured traits and SSR data (r = 0.20, p < 0.0003) based on the Mantel test. The PCA indicated that all vegetation SRIs and most water SRIs were grouped with measured traits in a positive direction and effectively identified the salt-tolerant RILs/cultivars. The PLSR models, which were based on all SRIs, accurately and robustly estimated the various morpho-physiological traits compared to using individual SRIs. The study suggests that various SRIs can be integrated with PLSR in wheat breeding programs as a cost-effective and non-destructive tool for phenotyping and screening large wheat populations for salt tolerance in a short time frame. This approach can replace the need for traditional morpho-physiological traits and accelerate the development of salt-tolerant wheat genotypes.

Adapting lipidomic sample processing methods for boars housed in commercial settings

Abstract Multiple reaction monitoring (MRM) profiling is a sensitive method of lipid screening that has the capability to distinguish between different fertility phenotypes in gilts. However, MRM profiling has not yet been utilized to evaluate fertility phenotypes in boars. Markers indicative of fertility status in boars would be valuable as inclusion of subfertile boars in breeding programs results in a loss of efficiency and negative economic consequences. In addition, semen samples for lipidomic analysis are transported in liquid nitrogen or on dry ice to suspend metabolic activity within the sperm cells, however, these cryopreservation techniques are not commonly available at commercial boar studs. Therefore, the objective of this study was to develop a method of sample processing for MRM profiling that suspends metabolic activity within semen without freezing the sample. Five, sexually mature boars of similar genetics enrolled in a commercial breeding program were collected for the study. Following collection, ejaculates were aliquoted into methanol to suspend metabolic activity and shipped to Purdue University overnight for lipid extraction. Lipids were extracted using the Bligh &amp; Dyer method and MRM profiling was used for lipid screening. A total of 329 ion transitions (MRMs) related to lipids were detected with most lipids being characterized as plasma membrane lipids (74%) which were comprised of phosphatidylcholines (40%), ceramides (16%), phosphatidylethanolamines (11%), and phosphatidylserines (7%). acylcarnitines (AC) represented approximately 8% of the ejaculate lipidome. Hierarchical cluster and principal component analysis revealed that boars have a distinct ejaculate lipidome profile based on major plasma membrane lipid classes. In addition, we observed that one boar was unique in his abundance of AC which are related to progressive motility and sperm cell metabolism. These results indicate that this method of sample processing for MRM profiling is suitable to be used to evaluate the lipidome of ejaculates from commercial boars and has potential for broader applications across different livestock species in commercial environments

Virulence of Puccinia coronata var avenae f. sp. avenae (oat crown rust) in Canada during 2016 to 2020 and comparison of extensive vs intensive sampling methods

Puccinia coronata var avenae f. sp. avenae (Pca), the causal fungus of crown rust of oats, is a significant threat to oat production in the eastern prairie region (Manitoba and eastern Saskatchewan; EPR), Ontario and Quebec (eastern Canada; EC), in Canada. Development of oat lines with effective resistance to Pca has been a priority for oat breeding programmes in Canada, and helped mitigate reductions in oat yield and quality. This requires knowledge of the virulence characteristics of the Pca population in Canada. Our objectives were to determine the incidence and severity of Pca in Canada, the presence and frequency of virulence and races in Pca populations and compare the traditional extensive sampling method (few isolates per field from many fields) to an intensive sampling method (many isolates per field from a few fields) for obtaining genetically diverse collections. The incidence and severity of crown rust of oat in Canada was lower in 2016 to 2020 than has been reported in previous years. Virulence to all the 24 Pc genes studied was observed over the 5 years in EC and the EPR. The most effective genes were Pc94, Pc98 and Pc101 in EC and Pc50, Pc96, Pc97 and Pc98 in the EPR. Approximately 81% of 424 races identified were of unique virulence phenotypes over the 5 years, indicating a highly variable Pca population in Canada. Races JTQG-91 and GTQG-91 were the most common races identified. Collections of Pca obtained using the extensive sampling method were observed to be more genetically diverse than collections obtained using the intensive sampling method in 2018 and 2020, but not in 2019.

Early and late responses to Fusarium Head blight in durum wheat: Focus on phenylpropanoid biosynthetic pathway

Durum wheat is among the cereal crops most susceptible to Fusarium Head Blight (FHB), a fungal disease that can lead to significant yield losses. Despite this, only limited research efforts have been directed towards understanding FHB resistance in durum wheat. Wheat grains naturally contain phenolic compounds, and anthocyanins are particularly present in the so-called pigmented wheat genotypes, such as purple pericarp ones. In this study the effects of the biotic stress caused by Fusarium graminearum infection on phenylpropanoid biosynthetic pathway in durum wheat spikes were explored, considering three genotypes with different susceptibility (including a purple pericarp genotype), and two time points (an early stage time point: 2 days post infection, and a late stage time point: 21 days post infection). At early infection stage, the F. graminearum infection triggered upregulation of all the considered genes involved in the phenylpropanoid pathway in the resistant genotype, while, in the purple pericarp genotype, the infection caused an increase in quercetin accumulation in the soluble fraction of spike extract. At late infection stage, the infection caused (in all the genotypes) a degradation of secondary cell wall and the release of the hydroxycinnamic acids esterified with arabinoxylans (ferulic acid and p-coumaric acid) and lignin-derived monomers (vanillic acid). Furthermore, chalcone synthase gene (CHS) and the transcription factor Ppm1 (Purple pericarp MYB 1) were boosted in the pigmented genotype due to infection at late infection stage. These findings contribute to the understanding of host-pathogen interactions for future breeding programs focused on improving FHB resistance in durum wheat varieties, with a particular focus on pigmented genotypes.

Assessment of Heritability and Genetic Advance for Yield and Yield Related Traits under Different Dates of Sowing of Bread Wheat (Triticum aestivum L.)

Wheat (Triticum aestivum L.) is a self-pollinating annual plant extensively grown as staple food source in the world. Information on the extent of heritability and genetic advance among different traits of bread wheat genotypes is essential to designing breeding strategies with the objective to estimate heritability and genetic advance for different characters of bread wheat genotypes. A total of 10 bread wheat genotypes were evaluated for 15 traits sown, three at different dates in 10 days interval The first on 30 November 2022, second on 10 December 2022, and third 20 December 2022 in a Randomized Block Design with three replications at Student Instruction Farm, C.S. Azad University of Agriculture and Technology, Kanpur-208002 (U.P.) during Rabi, 2022-23. in Randomized Block Design. High PCV and GCV were observed from biological yield, grain yield, plant height and productive tiller per plant high heritability estimate were recorded for grain yield per plant followed by biological yield per plant, plant height, days to 50% heading, days to maturity, number of productive tillers per plant, 1000-grain weight and number of grains per ear in both generations on individual and grain yield per plant followed by biological yield, number of productive tillers per plant, plant height, seed hardness, days to maturity in both generations on pooled basis. High genetic advance was observed for grain yield per plant and biological yield per plant in both the generation; seed hardness, number of productive tillers per plant in F1 generation and grain yield per plant and biological yield per plant in both the generation on pooled basis. Consequently, since additive gene action controls the phenotypic manifestation of certain features, those traits should receive special attention in wheat breeding programs. Grain yield will therefore be increased by direct selection for these features.

Multi‐Environment Analysis of Nutritional and Grain Quality Traits in Relation to Grain Yield Under Drought and Terminal Heat Stress in Bread Wheat and Durum Wheat

ABSTRACTHeat and drought are two important constraints to global wheat productivity; understanding the genotypic responses for quality parameters under harsh production conditions (drought and heat) is very important for developing nutrient‐dense wheat varieties. A set of 15 modern bread wheat (Triticum aestivum L. subsp. aestivum) and durum wheat (Triticum turgidum subsp. durum) cultivars were tested in nine environments, including three different production conditions (normal, heat and drought) during 2020–21. Genotype stability performance for yield, nutrition and quality parameters is assessed using multienvironment trials through AMMI and GGE Biplot analysis. We discovered intriguing stress dynamics in grain zinc content (Zn) and grain iron content (Fe). Under heat stress, zinc concentration increases but decreases under drought stress, while iron does the opposite. Selecting zinc, starch and kernel weight under terminal heat stress can boost yield. Protein content and yield are inversely related, making it difficult for breeders to optimise both traits. G × E interactions and stability indices across all environments have found genotypes with high‐yielding stable genotypes, G12 (MP1358) (42.09 ppm) and G5 (HI1544) (42.41 ppm) have high Fe content. G12 (MP1358) (14.98%) ranked highest in protein concentration. Meanwhile, for Zn content, G11 (MACS 4058) (45.23 ppm) and G15 (WH730) (42.44 ppm) were top performers across environments. G7 (HI 1636) and G12 (MP1358) stand out as a win‐win genotype for their high potential and stability in yield, protein, Zn and Fe content. Our study shows the complex relationships and possible suggestions for targeted breeding programmes under heat and drought stress conditions to improve wheat grain quality and micronutrient profiles without yield loss.

Association mapping analysis (AMA) for morpho-agronomic traits and leaf aromatic compounds using SSR markers in three types of Perilla crop collected from South Korea.

Perilla is a representative leafy vegetable in South Korea. As K-Food (Korean food) is in the spotlight around the world, there is also increasing interest in Western countries in Perilla crop, an annual plant belonging to the Lamiaceae family. To discover comprehensive information, including genetic and phylogenetic relationships among the 80 native Perilla accessions, using three types of data: simple sequence repeat (SSR) marker data, volatiles profile data, and morpho-agronomic data. This study conducted genotypic and phenotypic analyses on 80 Perilla accessions of three types (cultivated var. frutescens, weedy var. frutescens, weedy var. crispa) from South Korea. Five groups (G1-G5) of the 80 Perilla accessions of the three types were differentiated into two different clusters [genotype-based clustering (GTC) and phenotype-based clustering (PTC)] based on an aroma sensory phenotypic test. A total of 314 alleles were confirmed using 55 Perilla SSR primer sets, and genetic variation in the 80 Perilla accessions was evaluated. Among the three statistical analysis methods, principal coordinate analysis (PCoA) and GTC using data of the 55 Perilla SSR markers revealed perfectly consistent results, whereas PTC produced a total of six clusters. The 10 Perilla SSR markers associated with and significantly correlated with both biochemical and morphological characteristics were selected. These findings are expected to provide valuable information for developing global South Korean Perilla cultivars for further studies in Perilla crop breeding programs.

The Biological and Genetic Mechanisms of Fruit Drop in Apple Tree (Malus × domestica Borkh.)

The apple tree (Malus × domestica Borkh.) belongs to the Rosaceae. Due to its adaptability and tolerance to different soil and climatic conditions, it is cultivated worldwide for fresh consumption. The priorities of apple growers are high-quality fruits and stable yield for high production. About 90 to 95 percent of fruits should fall or be eliminated from apple trees to avoid overcropping and poor-quality fruits. Apple trees engage in a complex biological process known as yield self-regulation, which is influenced by several internal and external factors. Apple buds develop in different stages along the branches, and they can potentially give rise to new shoots, leaves, flowers, or fruit clusters. The apple genotype determines how many buds will develop into fruit-bearing structures and the capacity for yield self-regulation. Plant hormones such as ethylene, cytokinins, auxins, and gibberellins play a crucial role in regulating the fruit set, growth, and development, and the balance of these hormones influences the flowering intensity, fruit size, and fruit number on the apple tree. Apple growers often interfere in the self-regulation process by manually thinning fruit clusters. Different thinning methods, such as by hand, mechanical thinning, or applying chemical substances, are used for flower and fruit thinning. The most profitable in commercial orchards is the use of chemicals for elimination, but more environmentally sustainable solutions are required due to the European Green Deal. This review focuses on the biological factors and genetic mechanisms in apple yield self-regulation for a better understanding of the regulatory mechanism of fruitlet abscission for future breeding programs targeted at self-regulating yield apple varieties.

Genomic diversity study of highly crossbred cattle population in a Low and Middle Tropical environment

Milk production in tropical regions plays a crucial role both economically and socially. Typically, animals are utilized for dual purposes and are genetically obtained by an intense crossbreeding between Zebu and/or locally adapted breeds, alongside specialized breeds for dairy production. However, uncontrolled mating and crossbreeding may affect the establishment of an effective animal breeding program. The objective of this study was to evaluate Genomic diversity of highly crossbred cattle population in a Low and Middle Tropical environment. All sampled animals were genotyped using the Genessek GGP Bovine 100 chip (n = 859) and public genomic information from eight breeds were employed as reference. The genetic structure of the population was estimated using a Principal Component, Bayesian clustering and a linkage disequilibrium analysis. PCA results revealed that PC1 explained 44.39% of the variation, associated with the indicus/taurus differentiation, and PC2 explained 14.6% of the variation, attributed to the differentiation of Creole and European components. This analysis underscored a low population structure, attributed to the absence of genealogical tracking and the implementation of non-directed crossbreeding. The clustering shows an average contribution of Zebu, Creole, and European Taurine components in the population was 53.26%, 27.60%, and 19.13%, respectively. While an average LD of 0.096 was obtained for a maximum distance of 400 kb. The LD value was low in this population, probably due to the almost no selection applied and the recombination events that occurred during its development. These findings underscore the value of crossbreeding in tropical dairy production but emphasize the importance of directing the mattings.

A Review and Meta-Analysis of Genotype by Environment Interaction in Commercial Shrimp Breeding.

(1) Background: Genotype-by-environment interaction (G×E) can adversely impact genetic improvement programs. The presence of G×E is mainly measured as the genetic correlation between the same trait measured in different environments where departure from unity can be taken as presence of G×E. (2) Methods: To understand the extent of G×E in shrimp production, a review and meta-analysis was conducted using the results from 32 peer-reviewed studies. (3) Results: Of these, 22 G×E studies were conducted on Pacific white shrimp (Litopenaeus vannamei) with fewer studies reported in other shrimp species. The most frequently studied traits were growth and survival, with relatively few studies on traits of economic importance. The meta-analysis demonstrated a moderately high genetic correlation (rg = 0.72 ± 0.05) for growth, indicating low to moderate levels of G×E with some re-ranking of breeding values across environments. However, substantial G×E was evident for survival where only a moderate genetic correlation (rg = 0.58 ± 0.07) was observed for survival across different environments. A re-ranking of breeding values is likely for this trait and genetic improvement of shrimp for survival in one environment may not be effective in other environments. The results from ANOVA-based studies show that G×E accounted for 6.42 ± 1.05% and 7.13 ± 3.46% of the variation for growth and survival traits, respectively. (4) Conclusion: The significance of G×E necessitates tailored genetic improvement programs in commercial shrimp breeding. We discuss the scope and challenges of G×E for shrimp breeding programs, including opportunities of implementing G×E in genomic selection programs.