Conventional Breeding Programs Research Articles

Genomeprofile: Unveiling the genomic profile for livestock breeding through comprehensive SNP array-based genotyping.

In livestock breeding, single nucleotide polymorphism arrays have become a cornerstone of modern livestock breeding. SNP arrays facilitate the identification of genetic markers linked to economically important traits and provide a powerful tool for predicting breeding values. However, conventional breeding programs often overlook additional genomic features contained in the SNP array data that can provide valuable insights into the genetic diversity, copy number variation, inbreeding levels and potential challenges in breeding lines. Here we present genomeprofile, a tool using SNP array-based genomic data, offering a comprehensive profile of breeding animals including the identification of copy number variants and runs of homozygosity, and screening for aneuploidy. By integrating these features into the breeding landscape, genomeprofile enables a more comprehensive picture of genomic variation, ultimately enhancing precision breeding strategies. To illustrate the practicality and efficacy of genomeprofile, we applied the tool to a dataset of four pig breeding lines. The genomeprofile tool is a user-friendly tool that processes genotype data in finalreport or plink ped format efficiently into useful output. The output contains copy number variations, runs of homozygosity, selection signatures, aneuploidy and inbreeding per individual and across populations. This allows breeding companies and researchers to identify unique individuals or regions in the genome of interest based on routinely collected data.

Analysis of Fluorescently Labeled ISSR Markers to Reveal the Genetic Diversity of Cassava Varieties (Manihot esculenta Crantz) in the Kerala’s Tribal Area of India

The study Inter Simple Sequence Repeat (ISSR) molecular markers to genotype distinct cassava (Manihot esculenta Crantz) cultivars within tribal communities in Kerala, India. Fluorescent ISSR primers were labelled with 6-carboxyfluorescein and used for PCR amplification. The total number of bands produced was 72, of which 49 were found to be polymorphic markers; an average of 17 polymorphic bands was obtained per primer. The manuscript is a scientific validation of the traditional knowledge of tribal people regarding the diversity and wealth of cassava crops in the region, and this validation can therefore help in protecting the farmers right on a particular landrace that they cultivate. The technique used in the diversity analysis is a time-saving process as compared to conventional breeding programs for crop improvement. The data in the manuscript also supports similarity and differences of each variety to one another, which is analysed statistically with the molecular marker-based data generated. By examining genetic diversity at a high resolution, ISSR markers can provide valuable insights into the evolutionary dynamics of these cassava populations. This research contributes to the broader goal of enhancing agricultural sustainability and food security in tribal communities.

Social and biological innovations are essential to deliver transformative forest biotechnologies.

Forests make immense contributions to societies in the form of ecological services and sustainable industrial products. However, they face major challenges to their viability and economic use due to climate change and growing biotic and economic threats, for which recombinant DNA (rDNA) technology can sometimes provide solutions. But the application of rDNA technologies to forest trees faces major social and biological obstacles that make its societal acceptance a 'wicked' problem without straightforward solutions. We discuss the nature of these problems, and the social and biological innovations that we consider essential for progress. As case studies of biological challenges, we focus on studies of modifications in wood chemistry and transformation efficiency. We call for major innovations in regulations, and the dissolution of method-based market barriers, that together could lead to greater research investments, enable wide use of field studies, and facilitate the integration of rDNA-modified trees into conventional breeding programs. Without near-term adoption of such innovations, rDNA-based solutions will be largely unavailable to help forests adapt to the growing stresses from climate change and the proliferation of forest pests, nor will they be available to provide economic and environmental benefits from expanded use of wood and related bioproducts as part of an expanding bioeconomy.

The predicted benefits of genomic selection on pig breeding objectives.

The premise was tested that the additional genetic gain was achieved in the overall breeding objective in a pig breeding program using genomic selection (GS) compared to a conventional breeding program, however, some traits achieved larger gain than other traits. GS scenarios based on different reference population sizes were evaluated. The scenarios were compared using a deterministic simulation model to predict genetic gain in scenarios with and without using genomic information as an additional information source. All scenarios were compared based on selection accuracy and predicted genetic gain per round of selection for objective traits in both sire and dam lines. The results showed that GS scenarios increased overall response in the breeding objectives by 9% to 56% and 3.5% to 27% in the dam and sire lines, respectively. The difference in response resulted from differences in the size of the reference population. Although all traits achieved higher selection accuracy in GS, traits with limited phenotypic information at the time of selection or with low heritability, such as sow longevity, number of piglets born alive, pre- and post-weaning survival, as well as meat and carcass quality traits achieved the largest additional response. This additional response came at the expense of smaller responses for traits that are easy to measure, such as back fat and average daily gain in GS compared to the conventional breeding program. Sow longevity and drip loss percentage did not change in a favourable direction in GS with a reference population of 500 pigs. With a reference population of 1000 pigs or onwards, sow longevity and drip loss percentage began to change in a favourable direction. Despite the smaller responses for average daily gain and back fat thickness in GS, the overall breeding objective achieved additional gain in GS.

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 77.51kg 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.

Assessment of the usability of four molecular markers to ıdentify potato genotypes suitable for processing

The development of processing potato cultivars through a conventional breeding program requires a detailed analysis of post-harvest traits, which is a process that demands high labor and is often time-consuming. Visual selection by breeders is biased and difficult in the field, particularly for quality traits, which shows the importance of marker-assisted selection over conventional techniques. In this study, four allele-specific markers, AGPsS-9a, Stp23-8b, StpL-3e, and Pain1-8c, developed from tuber quality-related genes, were used to screen a breeding population of the NOHU for processing traits to check the efficiency of these markers in processing trait selection. Marker association with tuber quality trait results showed that AGPsS-9a (0, absent) and StpL-3e (0) individually were associated with increased chips quality, yet their individual presence improved the reducing sugar content. Further, Pain1-8c presence was associated with high levels of reducing sugar accumulation and lower dry matter content, specific gravity, and starch content. The marker combination Stp23-8b (0) and StpL-3e (0) reached statistical significance (P≤0.05) for better chips quality in the NOHU population. However, the markers (individual and combination) showed poor selection efficiency as a diagnostic marker, possibly reasoning from the multigenic inheritance of tuber quality traits, population structure, and environment.

Exploring natural genetic variation in photosynthesis-related traits of barley in the field.

Optimizing photosynthesis is considered an important strategy for improving crop yields to ensure food security. To evaluate the potential of using photosynthesis-related parameters in crop breeding programs, we measured chlorophyll fluorescence along with growth-related and morphological traits of 23 barley inbred lines across different developmental stages in field conditions. The photosynthesis-related parameters were highly variable, changing with light intensity and developmental progression of plants. Yet, the variation in photosystem II quantum yield observed among the inbred lines in the field largely reflected the variation in CO2 assimilation properties in controlled climate chamber conditions, confirming that the chlorophyll fluorescence-based technique can provide proxy parameters of photosynthesis to explore genetic variation under field conditions. Heritability (H2) of the photosynthesis-related parameters in the field ranged from 0.16 for the quantum yield of non-photochemical quenching to 0.78 for the fraction of open photosystem II center. Two parameters, the maximum photosystem II efficiency in the light-adapted state (H2=0.58) and the total non-photochemical quenching (H2=0.53), showed significant positive and negative correlations, respectively, with yield-related traits (dry weight per plant and net straw weight) in the barley inbred lines. These results indicate the possibility of improving crop yield through optimizing photosynthetic light use efficiency by conventional breeding programs.

Reviewing the essential roles of remote phenotyping, GWAS and explainable AI in practical marker-assisted selection for drought-tolerant winter wheat breeding.

Marker-assisted selection (MAS) plays a crucial role in crop breeding improving the speed and precision of conventional breeding programmes by quickly and reliably identifying and selecting plants with desired traits. However, the efficacy of MAS depends on several prerequisites, with precise phenotyping being a key aspect of any plant breeding programme. Recent advancements in high-throughput remote phenotyping, facilitated by unmanned aerial vehicles coupled to machine learning, offer a non-destructive and efficient alternative to traditional, time-consuming, and labour-intensive methods. Furthermore, MAS relies on knowledge of marker-trait associations, commonly obtained through genome-wide association studies (GWAS), to understand complex traits such as drought tolerance, including yield components and phenology. However, GWAS has limitations that artificial intelligence (AI) has been shown to partially overcome. Additionally, AI and its explainable variants, which ensure transparency and interpretability, are increasingly being used as recognised problem-solving tools throughout the breeding process. Given these rapid technological advancements, this review provides an overview of state-of-the-art methods and processes underlying each MAS, from phenotyping, genotyping and association analyses to the integration of explainable AI along the entire workflow. In this context, we specifically address the challenges and importance of breeding winter wheat for greater drought tolerance with stable yields, as regional droughts during critical developmental stages pose a threat to winter wheat production. Finally, we explore the transition from scientific progress to practical implementation and discuss ways to bridge the gap between cutting-edge developments and breeders, expediting MAS-based winter wheat breeding for drought tolerance.

Brinjal: Breeding and Genomics

Brinjal (Solanum melongena L.) also known as eggplant is an important solanaceous vegetable crop grown across tropical and subtropical regions of the world. India is the centre of origin of the crop, large diversity in the morphology of fruit and plant type exists in the country. Also, a large number of wild relatives is being utilized in breeding programs as a source of biotic and abiotic stress tolerance. Conventional breeding programs have focused on improving plant type and yield through the development of high-yielding varieties and hybrids. More recently, breeding for stress tolerance and enhanced nutritional content has gained importance. Genetic inheritance studies, mapping, molecular tools are enriching the crop improvement work. Of late, the availability of high-quality genome sequences has spurred functional analysis at the genome level augmenting molecular tools for marker-assisted selection. In the present article, attempt has been made to highlight the improvement work carried out from relevance of the crop diversity to genomic-level knowledge advancement. Future prospective in brinjal improvement having relevance in Indian context is also highlighted.

Potato: Breeding and Genomics

The commonly cultivated potato is a tetraploid and belongs to the species Solanum tuberosum, which includes two subspecies viz. ssp. tuberosum adapted to long days and ssp. Andigena adapted to short days. The conventional potato breeding programmes depend mainly on the identification of promising parental lines for making desired crosses, the creation of genetic variability through the crossing and subsequently the selection of desirable recombinants for further evaluation and vegetative propagation. During the last seven decades, Indian Council of Agricultural Research - Central Potato Research Institute (ICAR -CPRI) has developed and released as many as 69 improved varieties and one TPS population. These varieties cater to the need of the farmers across the country; and have superior agronomic attributes and resistance to different biotic and abiotic stresses. The somatic hybrids has been produced successfully by utilization of wild solanum species like S. etuberosum, S. cardiophyllam and S. pinnetisectum. Further, considerable work has been done in potato applying molecular biology and genomics approaches to address biotic and abiotic stress and quality traits.

Genome editing to re-domesticate and accelerate use of barley crop wild relatives

Climate change threatens global food security, but the biggest impact will be in arid, low social-economic regions. To improve food security, new breeding technologies (NBTs) could be implemented for re-domestication of crop wild relatives (CWR). CWR harbor many beneficial traits, but it is difficult to incorporate these traits into conventional breeding programs. Thus, although genebanks hold significant collections of CWR, their potential has yet to be reached. Using barley as an example, we describe how using genebank collections, digital sequence information and NBTs, re-domesticated barley can be produced with improved characteristics, while retaining the resilience and adaptation of the original material. Lastly, we highlight some obstacles that need to be overcome for re-domesticates to be adopted.

Genomic and Transcriptomic Approaches to Developing Abiotic Stress-Resilient Crops

In the realm of agriculture, a pressing concern remains the abiotic stresses, such as temperature fluctuation, drought, soil salinity, and heavy metal contamination. These adverse growth conditions hamper crop yields and global food security. In this review, we present a comprehensive examination of the recent advancements in utilizing genomics and transcriptomics, tools to enhance crop resilience against these stress factors. Genomics aids in the identification of genes responsive to stress, unravels regulatory networks, and pinpoints genetic variations linked to stress tolerance. Concurrently, transcriptomics sheds light on the intricate dynamics of gene expression during stress conditions, unearthing novel stress-responsive genes and signaling pathways. This wealth of knowledge shapes the development of stress-tolerant crop varieties, achieved through conventional breeding programs and state-of-the-art genetic engineering and gene editing techniques like CRISPR-Cas9. Moreover, the integration of diverse omics data and functional genomics tools empowers precise manipulation of crop genomes to fortify their stress resilience. In summary, the integration of genomics and transcriptomics holds substantial promise in elucidating the molecular mechanisms behind crop stress tolerance, offering a path towards sustainable agriculture and safeguarding food security amidst shifting environmental challenges.

Acceleration of wheat breeding: enhancing efficiency and practical application of the speed breeding system

BackgroundCrop breeding should be accelerated to address global warming and climate change. Wheat (Triticum aestivum L.) is a major food crop. Speed breeding (SB) and speed vernalization (SV) techniques for spring and winter wheat have recently been established. However, there are few practical examples of these strategies being used economically and efficiently in breeding programs. We aimed to establish and evaluate the performance of a breeder-friendly and energy-saving generation acceleration system by modifying the SV + SB system.ResultsIn this study, a four-generation advancement system for wheat (regardless of its growth habits) was established and evaluated using an energy-efficient extended photoperiod treatment. A glasshouse with a 22-hour photoperiod that used 10 h of natural sunlight and 12 h of LED lights, and minimized temperature control during the winter season, was successful in accelerating generation. Even with one or two field tests, modified speed breeding (mSB) combined with a speed vernalization system (SV + mSB) reduced breeding time by more than half compared to traditional field-based methods. When compared to the existing SV + SB system, the SV + mSB system reduced energy use by 80% to maintain a 22-hour photoperiod. Significant correlations were found between the SV + mSB and field conditions in the number of days to heading (DTH) and culm length (CL). Genetic resources, recombinant inbred lines, and breeding materials that exhibited shorter DTH and CL values under SV + mSB conditions showed the same pattern in the field.ConclusionsThe results of our SV + mSB model, as well as its practical application in wheat breeding programs, are expected to help breeders worldwide incorporate generation acceleration systems into their conventional breeding programs.

Double CRISPR knockout of pectin degrading enzymes improves tomato shelf‐life while ensuring fruit quality

Social Impact StatementTomato fruit is an important and popular commodity producing $95.62 billion worldwide. Tomato fruit losses in the supply chain vary between 25% and 42% depending on the production area and the availability of postharvest technologies. For many decades, conventional tomato breeding programs have focused on extending the shelf‐life of fresh‐market varieties. However, in many instances, consumer‐based quality traits were not considered a priority. Consumers are now demanding safe, nutrient‐rich, high‐flavor, and convenient fruit. Here, we demonstrate the use of gene editing to improve fruit shelf‐life and positively impact quality, which can help significantly reduce tomato fruit losses and meet consumer expectations.Summary Finding alternative ways to extend tomato fruit shelf‐life without reducing the quality is critical to ensure the accessibility and likeability of this commodity worldwide. Improving fruit firmness in tomato fresh‐market varieties directly impacts their shelf‐life potential. We simultaneously knocked out two pectin‐degrading enzymes, polygalacturonase (SlPG2a) and pectate lyase (SlPL), key for tomato fruit softening. We expected this gene‐editing approach to result in longer‐lasting fruit without negatively impacting consumer‐based quality attributes. By generating the double clustered regularly interspaced short palindromic repeats (CRISPR) knockout PGPL, we evaluated the combined functions of SlPG2a and SlPL on fruit quality, including shelf‐life attributes like firmness and water loss, fruit marketability, and disease incidence. We also assessed additional attributes impacting consumer acceptance, such as taste and aroma. We revealed that the enzymes SlPG2a and SlPL act additively, significantly impacting fruit firmness and shelf‐life, with the double CRISPR knockout PGPL outperforming the wild‐type fruit. Additionally, fruit quality traits, such as sugar: acid ratio, aroma volatiles, and skin color, were improved or not affected in the double CRISPR knockout PGPL compared to the wild‐type. The discoveries of this research provide new insights into the influence of pectin backbone degradation on fruit physiology and postharvest quality, which can be used in crop improvement programs to make fruit more resilient in the supply chain without compromising quality.

Toward Food Security in 2050: Gene Pyramiding for Climate-Smart Rice

The decline in crop productivity due to climate change is a major issue that threatens global food security and is the main challenge for breeders today in developing sustainable varieties with a wider tolerance to abiotic and biotic stresses. Breeding climate-smart rice (CSR) cultivars may be the best adaptation to climate change, with the potential to improve future food security and profitability for farmers in many nations. The main objective of this review is to highlight the direction of development of superior rice breeding from time to time, and various studies of new techniques of breeding methods for pyramiding various superior rice characteristics, especially characteristics related to abiotic stress, and to make a climate-suitable genotype that is resilient to climate change. For the design and strategy of the information search, a methodology was followed to compile and summarize the latest existing studies on rice breeding for abiotic stresses. The findings revealed that there is still an empty research gap in the context of supplying CSR products, which should be a priority for rice researchers in order to increase dissemination and ensure food security for future generations, particularly in climatically vulnerable agro-ecologies. And we conclude that, while technological innovation, specifically the integration of DNA markers and the genomic approach into conventional breeding programs, has made major contributions to the development of CSR, there is an urgent need to build strategic plans for the development of varieties with various stress tolerances.

Innovative approaches to integrating gender into conventional maize breeding: lessons from the Seed Production Technology for Africa project.

The integration of gender concerns in crop breeding programs aims to improve the suitability and appeal of new varieties to both women and men, in response to concerns about unequal adoption of improved seed. However, few conventional breeding programs have sought to center social inclusion concerns. This community case study documents efforts to integrate gender into the maize-focused Seed Production Technology for Africa (SPTA) project using innovation history analysis drawing on project documents and the authors' experiences. These efforts included deliberate exploration of potential gendered impacts of project technologies and innovations in the project's approach to variety evaluation, culminating in the use of decentralized on-farm trials using the tricot approach. Through this case study, we illustrate the power of active and respectful collaborations between breeders and social scientists, spurred by donor mandates to address gender and social inclusion. Gender integration in this case was further facilitated by open-minded project leaders and allocation of funding for gender research. SPTA proved to be fertile ground for experimentation and interdisciplinary collaboration around gender and maize breeding, and has provided proof of concept for larger breeding projects seeking to integrate gender considerations.

Integrating Non-photochemical Quenching (NPQ) Measurements for Identifying Flood-Tolerant Soybean Genotypes in the Era of Climate Change

Climate change has negatively affected agriculture worldwide, including soybean production. Studies have shown that rising temperatures and extreme weather events like droughts and floods significantly reduce soybean yields. Developing flood-tolerant soybean genotypes is crucial for ensuring food security. Conventional breeding programs are limited by laborious and imprecise visual rating methods for flooding tolerance identification. High-throughput platforms for plant phenotyping using imaging techniques offer potential solutions, but they lack information on underlying physiological mechanisms. Non-photochemical quenching (NPQ) is a molecular adaptation in photosynthesis that dissipates excess light energy, protecting plants from damage. This study aimed to integrate NPQ measurements into high-throughput phenotyping procedures to identify flooding-tolerant soybean genotypes. The study evaluated 160 soybean genotypes for flooding tolerance, identifying those with higher grain yield potential. Subsequently, ten genotypes were selected for monitoring NPQ responses under flooded conditions. Results showed that genotypes with higher grain yields also exhibited superior NPQ performance, suggesting a positive correlation between flooding tolerance and energy dissipation capacity. Among these genotypes, 58I60 RSF IPRO, 64HO130 I2X and BRS 525 displayed superior potential and could be further exploited in breeding efforts, considering their grain yield capacity, plant leaf area, and photoprotective capacity under flooding conditions. These findings suggest that integrating NPQ measurements into high-throughput phenotyping platforms can aid in identifying flood-tolerant soybean genotypes for breeding programs, leading to more resilient crops in the face of climate change. Further field studies are warranted to validate these hypotheses and improve crop models for future climate scenarios.

Exploring the linkage between root system architecture and grain iron content in wheat (Triticum aestivum L.)

Iron (Fe) is a vital element that is equally important for plants, animals, and humans. High Fe concentrations in wheat grains have reliance on plant roots, the hidden half of the plant with a role in nutrient mining. Enhanced grain Fe content of wheat can positively mitigate Fe malnutrition in poor populations. In the present study, 100 wheat varieties were studied to identify the root architectural characteristics in relation to grain Fe concentration. Germinated seeds were transplanted in a rhizobox kept in a standard nutrient solution and were harvested 12 days after transplanting. Roots were scanned and the images were processed using smart root software. A total of 12 wheat varieties, which had a vigorous and weak root system architecture (RSA), in combination with higher and lower Fe grain concentrations, were selected using principal component analysis. The uptake and translocation of Fe from root to shoot were determined through a pot experiment conducted for the above-mentioned 12 wheat varieties, with or without Fe fertilizer applied as FeSO4 to the soil. The data obtained from the pot experiment revealed that Dharabi-11 with vigorous RSA exhibited the highest grain Fe concentration (57.20 mg kg−1), low phytate concentration (6.50 mg kg−1), and maximum 1,000 grain weight, whereas Ujala-16 with weaker RSA had the lowest grain Fe concentration (13.33 mg kg−1), highest phytate concentration (9.07 mg kg−1), and lowest 1,000 grain weight. There were also varieties showing higher grain Fe concentrations with weaker RSA and vice versa. Although it is indicated that vigorous RSA leads to high grain Fe concentration, it is not the sole factor in high grain Fe concentration. Nevertheless, the results demonstrate that large genetic diversity is available among indigenous wheat germplasm in terms of grain Fe concentration and RSA. This information may be utilized in the development of new varieties through conventional and marker-assisted breeding programs using RSA traits for Fe biofortification in wheat, leading to the mitigation of Fe malnutrition.

Epigenomics: a new tool for the generation of climate resilient grapevines

Climate change is expected to increase the occurrence of extreme environmental conditions. Viticulture, as agriculture in general, is highly dependent on climatic conditions, not only for yield but also for fruit quality, which is the most important factor affecting produce value at the farm-gate. This demands the development of novel plant breeding techniques that will lead to the accelerated production of more resilient grape varieties, as conventional breeding programs for perennials are often prolonged. Recent research has suggested that environmental conditions can activate a memory of stress that could result in a primed response to subsequent stress events. This is a process capable of increasing plant’s resilience to abiotic stimuli, allowing plants to better adapt to extreme environmental conditions. While the effect of priming has been observed in many plants, the underlying mechanisms are puzzling and seldom studied in perennial crops. A large body of research has been developed in the last decade linking response to stress, stress priming, and memory of stress with epigenetic mechanisms. This understanding of plant epigenetics has opened the door to the application of epigenetics to crop improvement, such as the use of epigenetic breeding for the generation of more resilient crops. Perennial crop agriculture in general, and viticulture in particular, would benefit from more in-depth knowledge on epigenetic memory of stress.

Anthracnose Resistance in Legumes for Cropping System Diversification

Anthracnose, caused by hemibiotrophic Colletotrichum spp., is a destructive disease of legumes and many other crops worldwide. Colletotrichum spp. constitute one of the top 10 phytopathogenic fungi, infecting ∼3,000 plant species, attacking food and forage legume crops at all growth stages; including seed, seedlings, young, and mature plants; with consequent significant yield reductions. Presently, cultural practices and substantial use of synthetic fungicides are the most prevalent approaches for anthracnose management. In addition, there has been a strong focus toward developing advanced breeding lines and cultivars with improved anthracnose resistance. This has involved traditional breeding resulting in a wide range of anthracnose resistance resources being identified, particularly using advanced techniques within the common bean, soybean, lentil, mungbean, blackgram, and lupins. For instance, quantitative trait loci (QTLs) for resistance have been identified, enabling marker-assisted resistance breeding. More recently, molecular approaches; including genomics, transcriptomics, proteomics, and metabolomics; have been utilized to understand the pathogenesis and defense mechanisms involved in the Colletotrichum-legume interaction. Genetic manipulation through omics offers scope to better protect legumes from anthracnose by improving the efficiency of breeding programs. This review focuses on key pathogens (viz., C. truncatum, C. lentis, C. lupini, and C. lindemuthianum) causing anthracnose in legumes, their biology, and epidemiology, the disease management levers embracing progress with host resistance, genetic and breeding approaches, and highlights critical knowledge gaps in conventional and molecular breeding programs. We conclude that the ongoing progress toward developing breeding lines/cultivars/donors with improved resistance in legume plant responses against anthracnose using omics approaches offers novel insights into legume-anthracnose pathogen interactions and ensures more sustainable and effective disease management strategies for the future.