Breeding Programs Research Articles

Genetic diversity studies between Ipomoea wild species and cultivated sweet potato (Ipomoea batatas (L.) Lam.) using SSR markers

Sweet potato (Ipomoea batatas (L.) Lam) is one of the major tuber crops in Asian countries, including India, yet the interrelationship and genetic variability among the cultivar and its crop wild relatives remain obscure. The wild relatives of sweet potato represent a vital source of untapped genetic diversity in the breeding programs. In this study, a set of 12 Simple Sequence Repeats (SSR) markers were utilized to understand the extent of genetic diversity and relationship within and between 20 sweet potato accessions, 23 wild Ipomoea species and two Merremia species for utilization in breeding programmes. The SSR primers produced 84 polymorphic alleles within the range of 105-393 bp, collectively showing an average polymorphism of 94.5%. The average Polymorphic Information Content (PIC) value of 0.67 showed that all the primers were polymorphic in nature. Similarity coefficient based dendrogram and Principal Component Analysis (PCA) scatter plot clearly differentiated all the cultivars and wild species. The cluster dendrogram analysis revealed the close relationship of cultivars with I. triloba and I. trifida at a similarity index of 0.75. Our analysis showed a high degree of genetic variability within and between hexaploid sweet potato and diploid wild species, whereas lower within the cultivars, which shows that there is a high level of genetic diversity exists within the Ipomoea species for its utilization in breeding programs. Thus, the two wild species, I. trifida and I. triloba could be used in hybridization for improvement of sweet potato through ploidy manipulation.

Unravelling the role of key genes involved coffee leaf rust resistance

The biotrophic fungus Hemileia vastatrix is the pathogen responsible for coffee leaf rust, a devastating disease in several coffee-producing countries. Despite the importance of studying the interaction between Coffea and H. vastatrix, a more comprehensive understanding of the mechanisms involved in this pathosystem is necessary. The role of eight candidate genes was analyzed aiming at identifying and validating new important coffee resistance genes and understanding their interaction with H. vastatrix. These genes were identified in the most important sources of coffee resistance, the Híbrido de Timor CIFC 832/2 and CIFC 832/1. Previous works found six resistance genes and, in our research, other two new genes were identified in BAC clones and validated by RT-qPCR during compatible and incompatible interactions between Coffea and H. vastatrix. An interactome approach was performed using Coffea-H. vastatrix and Coffea-Coffea proteins to better understand the biological process and the interaction of the host-pathogen. Two networks of interactions from the compiled data were built focused on candidate genes associated with pre-haustorial resistance (12 and 24h.a.i) in coffee plants against the pathogen. The results showed, for the first time, differentially expressed proteins (DEPs) positively regulated in the incompatible interaction Coffea-H. vastatrix. These coffee proteins interact with each other and with secreted and/or transmembrane pathogen proteins. The obtained results also show that DEPs found are involved in important plant defense pathways such as pathways associated with the response to wounds, signaling, regulation of the innate immune response and the transmembrane receptor protein serine/threonine kinase pathway. The present work shows the involvement of genes in both pathogen recognition and signaling cascades, which act in pre-haustorial defense mechanisms of HdT coffee. Therefore, the candidate genes analyzed, together with the biological processes elucidated, have the potential to contribute to the development of new control strategies against the fungus H. vastatrix within coffee breeding programs aiming to develop cultivars with durable resistance.

Genotype by environment interaction and stability study in bread wheat (Triticum aestivum L.) genotypes in Guji Zone, Southern Ethiopia

Genotype by environment interaction and stability study in bread wheat (Triticum aestivum L.) genotypes in Guji Zone, Southern Ethiopia

Intraspecific karyotypic variability among 12 Indian accessions of Momordica charantia L. (bitter gourd): a medicinally important vegetable crop

Abstract Bitter gourd is a highly nutritious vegetable and important medicinal plant of economic importance. The present study is focused on cytogenetical characterization of 12 accessions of bitter gourd from different parts of India, aiming to differentiate their karyotypes and outline diagnostic features of the chromosomes within each accession's haploid complement. All the accessions possess 2n = 22 numbers of chromosomes. The chromosomes mainly were metacentric (16‒22 chromosomes), and the presence or absence of sub-metacentric (0‒6 chromosomes) chromosomes. The length of the chromosomes varied from 0.83 to 1.93 μm among the accessions studied. Significant differences were obtained for the seven intra-chromosomal indices and four inter-chromosomal indices among the accessions. Principal component analysis and unweighted pair group method with arithmetic mean study revealed relatively distant positioning of individuals that advocated intraspecific phylogenetic relationships and higher karyoevolutionary affinity in bitter gourd accessions. In the meiotic study, regular meiotic behaviour indicates genetic stability and a stable sexual cycle in different accessions. The percentage of pollen viability of all the studied accessions was very high (89.41–94.11%), and these accessions can be considered to be good pollinators. The results obtained will guide characterizing the elite genotypes, genotypes management and designing effective breeding programmes and crop improvement programmes.

Comparative analysis of key fiber characteristics in white Pima cotton (Gossypium barbadense L.): Native accessions from the Peruvian Amazon

AbstractThe fiber quality of cotton (Gossypium barbadense L.) native to the Peruvian Amazon region is one of the most versatile and essential natural fibers in the Peruvian textile industry. There is little information about the fiber quality traits of cotton genotypes native to the Peruvian Amazon region. This study investigated the fiber quality traits of Peruvian Pima cotton accessions native to the Amazon region of the La Convención Province, Cusco, Peru, to determine the lines with the greatest potential for improving fiber quality in cotton genetic breeding programs. A total of 14 cotton accessions with white fiber color, being 12 accessions of G. barbadense L. (Pima cotton) and two accessions of Gossypium sp. (unknown cotton), were analyzed. The fiber properties determined using the high volume instrument method included seven characteristics. All fiber properties were classified into five quality classes. The data on fiber quality properties were subjected to distribution, correlation, and canonical variable analysis. The results of fiber quality properties showed that the two accessions of Gossypium sp. (unknown cotton) can be promising options to be used as high‐quality fiber progenies in crop genetic breeding programs or can be cultivated by regional farmers for the purpose of producing cotton with high fiber quality. Future investigations could utilize other methods of fiber quality analysis and compare the fiber quality of these cotton accessions native to the Peruvian Amazon region with other cotton species grown worldwide to improve the understanding of Pima cotton fiber quality and its applicability in different contexts of the textile industries.

Decoding the Functionality of Plant Transcription Factors: Key Factors and Mechanisms.

Transcription factors (TFs) intricately govern cellular processes and responses to external stimuli by modulating gene expressions. TFs help plants to balance the trade-off between stress tolerance and growth, thus ensuring their long-term survival in challenging environments. Understanding the factors and mechanisms that define the functionality of plant TFs is of paramount importance for unravelling the intricate regulatory networks governing development, growth, and responses to environmental stimuli in plants. The article provides a comprehensive understanding of these factors and mechanisms defining the activity of TFs. Understanding the dynamic nature of TFs has practical implications for modern molecular breeding programs, as it provides insights into how to manipulate gene expression to optimize desired traits in crops. Moreover, recent studies also report the functional duality of transcription factors, highlighting their ability to switch between activation and repression modes, this represents an important mechanism for attuning gene expression. Here we discuss what possible reasons for dual nature of TFs are and how this duality instructs the cell fate decision during development, and fine-tunes stress responses in plants, enabling them to adapt to various environmental challenges.

Low frequency of the wild-type freezing-tolerance LsCBF7 allele among lettuce population suggests a negative selection during domestication and breeding.

Sustainable winter production in lettuce requires freezing tolerant varieties. This study identified a wild-type allele of LsCBF7 that could contribute to freezing tolerance improvement in lettuce. Lettuce is one of the most consumed vegetables globally. While ideally grown in 13-21°C, its cultivation extends into winter in milder climates. However, occasional freezing temperatures can significantly reduce yields. Therefore, the development of freezing-tolerant lettuce varieties has become a long-term goal of lettuce breeding programs. Despite its significance, our understanding of freezing tolerance in lettuce remains limited. Plants have evolved a coping mechanism against freezing, known as cold acclimation, whereby they can increase freezing tolerance when pre-exposed to low nonfreezing temperatures. The CBF pathway is well-known for its central role in cold acclimation. Previously, we identified 14CBFgenes in lettuce and discovered that one of them, LsCBF7, had a loss-of-function mutation. In this study, we uncovered that accessions from colder regions carried the wild-type allele ofLsCBF7and this allele likely contributed to increased freezing tolerance, with 14% of the lettuce population carrying this allele. Interestingly, in wild lettuce (L. serriola) that is considered a progenitor of cultivated lettuce, this wild-type allele was much more common, with a frequency of 90%. This finding suggests that this wild-type allele may have undergone negative selection during the domestication or breeding of lettuce. Our data strongly indicate that this allele could be linked to early bolting, an undesirable trait in lettuce, which may have driven the negative selection. While this wild-type allele shows promise for improving freezing tolerance in lettuce, it is crucial to decouple it from the early bolting trait to fully harness its potential in lettuce breeding.

Metabolic profile and gene expression pattern of cytokines and antioxidants markers during different physiological stages in Barki ewes

BackgroundIn livestock, identifying the physiological and reproductive stages is valuable in guiding management decisions related to nutrition, veterinary procedures, and breeding programs. To achieve this goal, a cohort of Barki ewes in this research underwent observation across three pivotal physiological conditions: pre-pregnancy, late pregnancy, and early lactation. Blood samples were collected to investigate the changes in serum metabolic profile as well as gene expression pattern of cytokines and antioxidants markers during these stages.ResultsOur results showed that during late pregnancy, there was a significant (P < 0.05) increase in red blood cells (11.9 ± 0.5 1012/L), hemoglobin (10.8 ± 0.4 g/dl) and neutrophils count (7 ± 0.1 109/L) with significant decrease (P < 0.05) of total white blood cell count (9.1 ± 0.05 109/L). The packed cell volume (%) and monocyte count showed a significant (P < 0.05) decrease during both late pregnancy and early lactation stages. The serum concentrations of glucose, cholesterol, GSH, GPx, SOD and catalase displayed significant (P < 0.05) decrease during late pregnancy and early-lactation. Notably, during late pregnancy, there was a significant (P < 0.05) increase in the serum concentrations of albumin, globulin, urea, IGF-1, and malondialdehyde with significant decrease (P < 0.05) of total protein (4.9 ± 0.08 g/dl). Additionally, during early lactation, there was a significant (P < 0.05) increase in the serum levels of non-esterified fatty acids, triiodothyronine (T3), and thyroxin (T4). The gene expression profiles of cytokines (IL-4, IL-6, IL-8, and NFKB) were decreased in the ewes during late pregnancy compared to pre-pregnant and early lactation stages. In addition, the expression profile of antioxidant genes (SOD, CAT, GPX, and Nrf2) was significantly upsurged in the non-pregnant ewes compared to late pregnancy and early lactation ones.ConclusionsThe results concluded that different physiological status significantly affects the blood metabolic profile and gene expression pattern in Barki sheep. Our findings can be helpful in monitoring animal health and applying in breeding programs of Barki sheep under harsh environmental conditions.

The Dark Side of the pollen: BSA-seq identified genomic regions linked to male sterility in globe artichoke

Globe artichoke (Cynara cardunculus var. scolymus; 2n = 2x = 34) is a food crop consumed for its immature flower heads. Traditionally, globe artichoke varietal types are vegetatively propagated. However, seed propagation makes it possible to treat the crop as annual, increasing field uniformity and reducing farmers costs, as well as pathogens diffusion. Despite globe artichoke’s significant agricultural value and the critical role of heterosis in the development of superior varieties, the production of hybrids remains challenging without a reliable system for large-scale industrial seed production. Male sterility (MS) presents a promising avenue for overcoming these challenges by simplifying the hybridization process and enabling cost-effective seed production. However, within the Cynara genus, genic male sterility has been linked to three recessive loci in globe artichoke, with no definitive genetic mechanism elucidated to date. A 250 offsprings F2 population, derived from a cross between a MS globe artichoke and a male fertile (MF) cultivated cardoon (C. cardunculus var. altilis) and fitting a monogenic segregation model (3:1), was analyzed through BSA-seq, aiming at the identification of genomic regions/genes affecting male sterility. Four QTL regions were identified on chromosomes 4, 12, and 14. By analyzing the sequence around the highest pick on chromosome 14, a cytochrome P450 (CYP703A2) was identified, carrying a deleterious substitution (R/Q) fixed in the male sterile parent. A single dCAPS marker was developed around this SNP, allowing the discrimination between MS and MF genotypes within the population, suitable for applications in plant breeding programs. A 3D model of the protein was generated by homology modeling, revealing that the mutated amino acid is part of a highly conserved motif crucial for protein folding.

Future of durum wheat research and breeding: Insights from early career researchers.

Durum wheat (Triticum turgidum ssp. durum) is globally cultivated for pasta, couscous, and bulgur production. With the changing climate and growing world population, the need to significantly increase durum production to meet the anticipated demand is paramount. This review summarizes recent advancements in durum research, encompassing the exploitation of existing and novel genetic diversity, exploration of potential new diversity sources, breeding for climate-resilient varieties, enhancements in production and management practices, and the utilization of modern technologies in breeding and cultivar development. In comparison to bread wheat (T. aestivum), the durum wheat community and production area are considerably smaller, often comprising many small-family farmers, notably in African and Asian countries. Public breeding programs such as the International Maize and Wheat Improvement Center (CIMMYT) and the International Center for Agricultural Research in the Dry Areas (ICARDA) play a pivotal role in providing new and adapted cultivars for these small-scale growers. We spotlight the contributions of these and others in this review. Additionally, we offer our recommendations on key areas for the durum research community to explore in addressing the challenges posed by climate change while striving to enhance durum production and sustainability. As part of the Wheat Initiative, the Expert Working Group on Durum Wheat Genomics and Breeding recognizes the significance of collaborative efforts in advancing toward a shared objective. We hope the insights presented in this review stimulate future research and deliberations on the trajectory for durum wheat genomics and breeding.

Community-based breeding programs can realize sustainable genetic gain and economic benefits in tropical dairy cattle systems

Implementing an appropriate breeding program is crucial to control fluctuation in performance, enhance adaptation, and further improve the crossbred population of dairy cattle. Five alternative breeding programs (BPs) were modeled considering available breeding units in the study area, the existing crossbreeding practices, and the future prospects of dairy research and development in Ethiopia. The study targeted 143,576 crossbred cows of 54,822 smallholder households in the Arsi, West Shewa, and North Shewa zones of the Oromia Region, as well as the North Shewa zone of the Amhara Region. The alternative BPs include conventional on-station progeny testing (SPT), conventional on-farm progeny testing (FPT), conventional on-station and on-farm progeny testing (SFPT), genomic selection (GS), and genomic progeny testing (GPT). Input parameters for modeling the BPs were taken from the analysis of long-term data obtained from the Holetta Agricultural Research Center and a survey conducted in the study area. ZPLAN+ software was used to predict estimates of genetic gain (GG) and discounted profit for goal traits. The predicted genetic gains (GGs) for milk yield (MY) per year were 34.52 kg, 49.63 kg, 29.35 kg, 76.16 kg, and 77.51 kg for SPT, FPT, SFPT, GS, and GPT, respectively. The GGs of the other goal traits range from 0.69 to 1.19 days per year for age at first calving, from 1.20 to 2.35 days per year for calving interval, and from 0.06 to 0.12 days per year for herd life. Compared to conventional BPs, genomic systems (GPT and GS) enhanced the GG of MY by 53%–164%, reduced generation interval by up to 21%, and improved the accuracy of test bull selection from 0.33 to 0.43. The discounted profit of the BPs varied from 249.58 Ethiopian Birr (ETB, 1 USD = 39.55696 ETB) per year in SPT to 689.79 ETB per year in GS. Genomic selection outperforms SPT, SFPT, and FPT by 266, 227%, and 138% of discounted profit, respectively. Community-based crossbreeding accompanied by GS and gradual support with progeny testing (GPT) is recommended as the main way forward to attain better genetic progress in dairy farms in Ethiopia and similar scenarios in other tropical countries.

Improvement of cool-season food legumes for adaptation to intercropping systems: breeding faba bean for intercropping with durum wheat as a case study

Although the transition toward a more sustainable agricultural system is sparking the interest of scientists and farmers around the globe, breeding programs are still focusing on optimizing cultivars intended for the monoculture system, and most cultivars available on the market are not suitable for intercropping. The incorporation of versatile cool-season food legumes (CSFLs) in the intercropping system is a promising way toward more diversified and sustainable cropping systems. However, as the selection of good-performing cultivars under sole cropping does not always lead to a good performance in intercropping, the development of an alternative breeding scheme for intercropping is now a necessity. The case study of faba bean–wheat intercropping was used to select for traits associated with better performance of faba bean, resulting in identifying the combined grain yield, 100-seed weight, number of pods per plant, and canopy height as key traits for faba bean–wheat intercropping suitability. Incorporating these traits in the breeding programs would be the cornerstone of the prospective transition.

Stability Analysis and Genetic Variability in Buckwheat (Fagopyrum esculentum Moench.)

Aims: To estimate the genetic variability and to identify the stable buckwheat genotype for growth and yield parameters. Study Design: Eberhart and Russell model. Place and Duration of Study: Department of Plantation, Spices, Medicinal and Aromatic Crops, College of Horticulture, Bagalkot, Karnataka during Jan-April 2021-2022. Methodology: Fifteen genotypes of buckwheat were assessed for stability parameters for 15 characters across three environments i.e, full dose of recommended fertilizer (RDF), 3/4th dose of RDF and 1/2nd dose of RDF. The pooled data of these environments were used for estimation of genetic variability. Results: The heritability estimates were moderate to high for all the characters. The genetic advance over mean was found highest for number of clusters per cyme (35.05%), seed yield per plot (32.68%) and seed yield per hectare (32.72%). The genotype EC-104035 was found stable for seed yield per plant, per plot and hectare, EC-386667, EC-3222, Nilgiri local, PRB-1 and Sangla B-460 for thousand seed weight, IC-313134 and EC-3222 for plant height at 45 days after sowing and at harvest, Shimla B-1 for plant height at 15 days after sowing, IC-49671, IC-274429 and Sangla B-460 for number of branches at 30 DAS, PRB-1 for days to first flowering and Nilgiri local for days to 50 percent flowering. Conclusion: The genotypes stable for more traits with high genetic variability, will be considered for future breeding program.

Increasing sorghum yields for smallholder farmers in Mali: the evolution towards a context-driven, on-farm, gender-responsive sorghum breeding program

This case study explores a decades long evolution towards a gender-responsive sorghum breeding program in Mali. With known disparities in men and women’s access to the resources that improve agricultural productivity and evidence that gender roles and responsibilities shape knowledge and preferences about varieties, there is need for methods that support gender-responsive processes in plant breeding programs. Gender-sensitive and gender-responsive approaches in plant breeding may increase varietal options available to diverse end-users, increase adoption, and limit negative impacts on vulnerable populations. We assess a participatory plant breeding program in Mali to identify determinants of gender-responsive breeding programs. The analysis uses a case study methodology that draws upon project reports, theses, articles, and experiential knowledge to understand how the sorghum breeding program transitioned over time. This case study details (a) more than a decade of sorghum breeding activities and research that led to (b) the inclusion of women in participatory plant breeding, culinary tests, and large-scale participatory selection in on-farm trials, reaching hundreds of women each year and (c) iterative co-learning processes to develop preferred sorghum varieties and increase sorghum yields on men and women’s fields. Analyses indicated that collaborations among many institutions on-farm with community actors, research across various disciplines such as agronomy and social sciences, context-specific breeding, and long-term funding were essential to increasing gender sensitivity and responsive in the breeding efforts.

Genotype by year interaction for selected traits in sweet maize (Zea maize L.) hybrids using AMMI model

This study investigated genotype × environment interactions for the stability of expression of four productivity traits (cobs yield, cobs I class trade share, lend of cobs and fulfilment of cobs) of sweet maize hybrids (Zea mays L.). The additive main effects and multiplicative interaction (AMMI) model was employed to assess genotype × environment interaction. AMMI stability value was used to evaluate both stability and genotype. The genotype selection index was calculated for each hybrid, incorporating both the average trait value and the stability index. Ten sweet maize hybrids were evaluated: Golda, GSS 1453, GSS 3071, GSS 5829, GSS 8529, Overland, Noa, Shinerock, Sindon, and Tessa. Trials were ran conducted over four vegetative seasons at a single location in the Wielkopolska region using replicated field experiments. The AMMI model revealed significant genotypic and environmental effects for all analyzed traits. Based on their superior stability and favorable average trait values, both the Golda cultivar and the GSS 3071 hybrid are recommended for further breeding program inclusion.

Accuracy of genomic prediction using multiple Atlantic salmon populations

BackgroundThe accuracy of genomic prediction is partly determined by the size of the reference population. In Atlantic salmon breeding programs, four parallel populations often exist, thus offering the opportunity to increase the size of the reference set by combining these populations. By allowing a reduction in the number of records per population, multi-population prediction can potentially reduce cost and welfare issues related to the recording of traits, particularly for diseases. In this study, we evaluated the accuracy of multi- and across-population prediction of breeding values for resistance to amoebic gill disease (AGD) using all single nucleotide polymorphisms (SNPs) on a 55K chip or a selected subset of SNPs based on the signs of allele substitution effect estimates across populations, using both linear and nonlinear genomic prediction (GP) models in Atlantic salmon populations. In addition, we investigated genetic distance, genetic correlation estimated based on genomic relationships, and persistency of linkage disequilibrium (LD) phase across these populations.ResultsThe genetic distance between populations ranged from 0.03 to 0.07, while the genetic correlation ranged from 0.19 to 0.99. Nonetheless, compared to within-population prediction, there was limited or no impact of combining populations for multi-population prediction across the various models used or when using the selected subset of SNPs. The estimates of across-population prediction accuracy were low and to some extent proportional to the genetic correlation estimates. The persistency of LD phase between adjacent markers across populations using all SNP data ranged from 0.51 to 0.65, indicating that LD is poorly conserved across the studied populations.ConclusionsOur results show that a high genetic correlation and a high genetic relationship between populations do not guarantee a higher prediction accuracy from multi-population genomic prediction in Atlantic salmon.

Integrating Omics Approaches for Climate-Resilient Crops: A Comprehensive Review

Climate change is a looming threat to global agriculture, impacting temperature, rainfall patterns, pest dynamics, and soil quality. These challenges transcend numerous crops vital for global food security. Drought, soil acidity, and nutrient fluctuations induced by climate change impede crop productivity, necessitating the development of breeding strategies to produce climate-resilient varieties. This review delves into the integration of omics approaches, including genomics, transcriptomics, proteomics, and metabolomics, to bolster breeding programs across diverse crops. By harnessing high-throughput technologies, researchers gain insights into the genetic and molecular mechanisms underlying traits such as stress resistance, yield, and disease tolerance. The cultivation of elite cultivars with enhanced stress tolerance is paramount for sustainable agriculture in the face of climate change. Various breeding approaches, encompassing functional genomics and mutagenomics, are explored alongside the application of genome editing tools like CRISPR/Cas9 and TALEN for targeted trait enhancement. Through the integration of multi-omics data, novel genetic targets are unearthed, facilitating the development of crop varieties resilient to climate-induced stressors beyond maize. This review underscores the significance of multi-omics in crop breeding and highlights strides made toward climate-resilient crop production. Understanding crop responses to abiotic stresses induced by climate change is imperative for the development of resilient varieties. The integration of modern genetics into classical breeding methods aims to cultivate stress-resistant cultivars, mitigating food security risks. Multi-omics approaches play pivotal roles in unraveling crop performance and stress tolerance mechanisms under diverse environmental conditions. Moving forward, the integration of multi-omics approaches will pinpoint candidate genes and pathways, enabling precision breeding to enhance crop performance amidst changing climates. These endeavors will propel the advancement of climate-resilient crops, safeguarding global food security in the face of climate change's challenges.

Response of mungbean genotypes for resistance against mungbean yellow mosaic virus

Mungbean yellow mosaic virus (MYMV) is an important viral disease across mungbean growing areas and causes severe yield loss in mungbean especially during the spring/summer season. The present study was envisaged to identify MYMV donors in mungbean. A total of 104 mungbean genotypes were evaluated for MYMV under natural field conditions during summer, 2019. The results revealed that MYMV severity ranged from 0% to 100% among mungbean genotypes. Out of 104 genotypes, 32 genotypes were completely free from MYMV, two genotypes exhibited resistant reaction (R), 22 genotypes were found moderately resistant (MR) and the remaining 48 genotypes were susceptible to highly susceptible reaction to MYMV. Thus, the identified 34 promising lines of mungbean were further evaluated against MYMV along with susceptible check DGGV-2 under epiphytotic conditions during the summer of 2020 and 2021. Pooled data of MYMV over the two years indicated that six genotypes namely, IPM-1205-2, IPM-2-14, IPM-410-3, IPM14-10, IPM-205-7 and IPM-1604-1 were showed stability for MYMV resistance. These identified stable resistant genotypes will serve as potential donors for the mungbean breeding program to develop resistance cultivars.

Genome-wide association study and genomic selection of spike-related traits in bread wheat.

Identification of 337 stable MTAs for wheat spike-related traits improved model accuracy, and favorable alleles of MTA259 and MTA64 increased grain weight and yield per plant. Wheat (Triticum aestivum L.) is one of the three primary global, staple crops. Improving spike-related traits in wheat is crucial for optimizing spike and plant morphology, ultimately leading to increased grain yield. Here, we performed a genome-wide association study using a dataset of 24,889 high-quality unique single-nucleotide polymorphisms (SNPs) and phenotypic data from 314 wheat accessions across eight diverse environments. In total, 337 stable and significant marker-trait associations (MTAs) related to spike-related traits were identified. MTA259 and MTA64 were consistently detected in seven and six environments, respectively. The presence of favorable alleles associated with MTA259 and MTA64 significantly reduced wheat spike exsertion length and spike length, while enhancing thousand kernel weight and yield per plant. Combined gene expression and network analyses identified TraesCS6D03G0692300 and TraesCS6D03G0692700 as candidate genes for MTA259 and TraesCS2D03G0111700 and TraesCS2D03G0112500 for MTA64. The identified MTAs significantly improved the prediction accuracy of each model compared with using all the SNPs, and the random forest model was optimal for genome selection. Additionally, the eight stable and major MTAs, including MTA259, MTA64, MTA66, MTA94, MTA110, MTA165, MTA180, and MTA164, were converted into cost-effective and efficient detection markers. This study provided valuable genetic resources and reliable molecular markers for wheat breeding programs.

Phased Telomere-to-Telomere Reference Genome and Pangenome Reveal an Expansion of Resistance Genes during Apple Domestication.

The cultivated apple (Malus domestica Borkh.) is a cross-pollinated perennial fruit tree of great economic importance. Previous versions of apple reference genomes were unphased, fragmented, and lacked comprehensive insights into the highly heterozygous genome, which impeded genetic studies and breeding programs in apple. In this study, we assembled a haplotype-resolved telomere-to-telomere reference genome for the diploid apple cultivar Golden Delicious. Subsequently, we constructed a pangenome based on twelve assemblies from wild and cultivated apples to investigate different types of resistance gene analogs (RGAs). Our results revealed the dynamics of the gene gain and loss events during apple domestication. Compared with cultivated species, more gene families in wild species were significantly enriched in oxidative phosphorylation, pentose metabolic process, responses to salt, and abscisic acid biosynthesis process. Interestingly, our analyses demonstrated a higher prevalence of RGAs in cultivated apples than their wild relatives, partially attributed to segmental and tandem duplication events in certain RGAs classes. Other types of structural variations, mainly deletions and insertions, have affected the presence and absence of TIR-NB-ARC-LRR (TNL), NB-ARC-LRR (NL), and CC-NB-ARC-LRR (CNL) genes. Additionally, hybridization/introgression from wild species has also contributed to the expansion of resistance genes in domesticated apples. Our haplotype-resolved T2T genome and pangenome provide important resources for genetic studies of apples, emphasizing the need to study the evolutionary mechanisms of resistance genes in apple breeding programs.