Marker-assisted selection: an approach for precision plant breeding in the twenty-first century

CRISPR-Cas9-mediated Editing of GmARM Improves Resistance to Multiple Stresses in Soybean

The growth and development of soybean plants can be affected by both abiotic and biotic stressors, such as saline-alkali stress and Phytophthora root rot. In this study, we identified a stress-related gene-GmARM-whose promoter contained several hormone-response and stress-regulatory elements, including ABRE, TCA element, STRE, and MBS. qRT-PCR analysis showed that the expression of GmARM was the highest in seeds at 55 days after flowering. Furthermore, this gene was upregulated after exposure to saline-alkali stress and Phytophthora root rot infection at the seedling stage. Thus, we generated GmARM mutants using the CRISPR-Cas9 system to understand the role of this gene in stress response. T3 plants showed significantly improved salt tolerance, alkali resistance, and disease resistance, with a significantly higher survival rate than the wildtype plants. Moreover, mutations in GmARM affected the expression of related stress-resistance genes, indicating that GmARM mutants achieved multiple stress tolerance. Therefore, this study provides a foundation for further exploration of the genes involved in resistance to multiple stresses in soybean that can be used for breeding multiple stress-resistance soybean varieties.

Introgression of OsAP47 by marker-assisted selection enhanced resistance against southern rice black-streaked dwarf virus disease

Southern rice black-streaked dwarf virus disease (SRBSDVD) is the most destructive viral disease in rice. In order to breeding resistant cultivars, Insertion-Deletion (InDel) markers were developed linked to OsAP47, the first isolated major resistance gene against SRBSDVD. Marker-assisted selection (MAS) was conducted to introduce this gene into the commercial variety. A rice line carrying homozygous resistance allele of OsAP47 was selected and named Kanghei No. 201 (KH201). Evaluated by artificial inoculation, KH201 showed significantly higher resistance than the recurrent parent Suxiu No.867 (SX867). And no significant differences were detected for KH201 in the yield-related components, including spikelets per panicle (SPP), ripened grains per panicle (RGPP), 1000-grain weight (TGW) and panicles per square meter (PPSM), leading to stable theoretical yield. The results indicated that introgression of OsAP47 improved rice resistance and can avoid yield losses produced by SRBSDVD. KH201 was demonstrated as a resistance material that could be used in rice breeding.

Exploring Disease Resistance in Pepper (Capsicum spp.) Germplasm Collection Using Fluidigm SNP Genotyping

This study utilized a diverse Capsicum accessions (5658) sourced from various species and geographical regions, deposited at the National Agrobiodiversity Center, Genebank. We employed 19 SNP markers through a Fluidigm genotyping system and screened these accessions against eight prevalent diseases of pepper. This study revealed accessions resistant to individual diseases as well as those exhibiting resistance to multiple diseases, including bacterial spot, anthracnose, powdery mildew, phytophthora root rot, and potyvirus. The C. chacoense accessions were identified as resistant materials against bacterial spot, anthracnose, powdery mildew, and phytophthora root rot, underscoring the robust natural defense mechanisms inherent in the wild Capsicum species and its potential uses as sources of resistance for breeding. C. baccatum species also demonstrated to be a promising source of resistance to major pepper diseases. Generally, disease-resistant germplasm has been identified from various Capsicum species. Originating from diverse locations such as Argentina, Bolivia, and the United Kingdom, these accessions consistently demonstrated resistance, indicating the widespread prevalence of disease-resistant traits across varied environments. Additionally, we selected ten pepper accessions based on their resistance to multiple diseases, including CMV, Phytophthora root rot, potyviruses, and TSWV, sourced from diverse geographical regions like Hungary, Peru, the United States, and the Netherlands. This comprehensive analysis provides valuable insights into disease resistance in Capsicum, crucial for fostering sustainable agricultural practices and advancing crop improvement through breeding strategies.

Development of Novel KASP Markers for Improved Germination in Deep-Sown Direct Seeded Rice

BACKGROUND

The lack of stable-high yielding and direct-seeded adapted varieties with better germination ability from deeper soil depth and availability of molecular markers are major limitation in achieving the maximum yield potential of rice under water and resource limited conditions. Development of high-throughput and trait-linked markers are of great interest in genomics-assisted breeding. The aim of present study was to develop and validate novel KASP (Kompetitive Allele-Specific PCR) markers associated with traits improving germination and seedling vigor of deep sown direct seeded rice (DSR).

RESULTS

Out of 58 designed KASP assays, four KASP assays did not show any polymorphism in any of the eleven genetic backgrounds considered in the present study. The 54 polymorphic KASP assays were then validated for their robustness and reliability on the F1s plants developed from eight different crosses considered in the present study. The third next validation was carried out on 256 F3:F4 and 713 BC3F2:3 progenies. Finally, the reliability of the KASP assays was accessed on a set of random 50 samples from F3:F4 and 80-100 samples from BC3F2:3 progenies using the 10 random markers. From the 54 polymorphic KASP, based on the false positive rate, false negative rate, KASP utility in different genetic backgrounds and significant differences in the phenotypic values of the positive (desirable) and negative (undesirable) traits, a total of 12 KASP assays have been selected. These 12 KASP include 5 KASP on chromosome 3, 1 on chromosome 4, 3 on chromosome 7 and 3 on chromosome 8. The two SNPs lying in the exon regions of LOC_Os04g34290 and LOC_Os08g32100 led to non-synonymous mutations indicating a possible deleterious effect of the SNP variants on the protein structure.

CONCLUSION

The present research work will provide trait-linked KASP assays, improved breeding material possessing favourable alleles and breeding material in form of expected pre-direct-seeded adapted rice varieties. The marker can be utilized in introgression program during pyramiding of valuable QTLs/genes providing adaptation to rice under DSR. The functional studies of the genes LOC_Os04g34290 and LOC_Os08g32100 possessing two validated SNPs may provide valuable information about these genes.

Genetic insights into agronomic and morphological traits of drug-type cannabis revealed by genome-wide association studies

Cannabis sativa L., previously concealed by prohibition, is now a versatile and promising plant, thanks to recent legalization, opening doors for medical research and industry growth. However, years of prohibition have left the Cannabis research community lagging behind in understanding Cannabis genetics and trait inheritance compared to other major crops. To address this gap, we conducted a comprehensive genome-wide association study (GWAS) of nine key agronomic and morphological traits, using a panel of 176 drug-type Cannabis accessions from the Canadian legal market. Utilizing high-density genotyping-by-sequencing (HD-GBS), we successfully generated dense genotyping data in Cannabis, resulting in a catalog of 800 K genetic variants, of which 282 K common variants were retained for GWAS analysis. Through GWAS analysis, we identified 18 markers significantly associated with agronomic and morphological traits. Several identified markers exert a substantial phenotypic impact, guided us to putative candidate genes that reside in high linkage-disequilibrium (LD) with the markers. These findings lay a solid foundation for an innovative cannabis research, leveraging genetic markers to inform breeding programs aimed at meeting diverse needs in the industry.

Advances in genomics and genome editing for improving strawberry (Fragaria ×ananassa)

The cultivated strawberry, Fragaria ×ananassa, is a recently domesticated fruit species of economic interest worldwide. As such, there is significant interest in continuous varietal improvement. Genomics-assisted improvement, including the use of DNA markers and genomic selection have facilitated significant improvements of numerous key traits during strawberry breeding. CRISPR/Cas-mediated genome editing allows targeted mutations and precision nucleotide substitutions in the target genome, revolutionizing functional genomics and crop improvement. Genome editing is beginning to gain traction in the more challenging polyploid crops, including allo-octoploid strawberry. The release of high-quality reference genomes and comprehensive subgenome-specific genotyping and gene expression profiling data in octoploid strawberry will lead to a surge in trait discovery and modification by using CRISPR/Cas. Genome editing has already been successfully applied for modification of several strawberry genes, including anthocyanin content, fruit firmness and tolerance to post-harvest disease. However, reports on many other important breeding characteristics associated with fruit quality and production are still lacking, indicating a need for streamlined genome editing approaches and tools in Fragaria ×ananassa. In this review, we present an overview of the latest advancements in knowledge and breeding efforts involving CRISPR/Cas genome editing for the enhancement of strawberry varieties. Furthermore, we explore potential applications of this technology for improving other Rosaceous plant species.

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.

Genome-wide QTL mapping for agronomic traits in the winter wheat cultivar Pindong 34 based on 90K SNP array

Introduction

Agronomic traits are key components of wheat yield. Exploitation of the major underlying quantitative trait loci (QTLs) can improve the yield potential in wheat breeding.

Methods

In this study, we constructed a recombinant inbred line (RIL) population from Mingxian 169 (MX169) and Pindong 34 (PD34) to determine the QTLs for grain length (GL), grain width (GW), grain length-to-width ratio (LWR), plant height (PH), spike length (SL), grain number per spike (GNS), and the thousand grain weight (TGW) across four environments using wheat 90K SNP array.

Results

A QTL associated with TGW, i.e., QTGWpd.swust-6BS, was identified on chromosome 6B, which explained approximately 14.1%-16.2% of the phenotypic variation. In addition, eight QTLs associated with GL were detected across six chromosomes in four different test environments. These were QGLpd.swust-1BL, QGLpd.swust-2BL, QGLpd.swust-3BL.1, QGLpd.swust-3BL.2, QGLpd.swust-5DL, QGLpd.swust-6AL, QGLpd.swust-6DL.1, and QGLpd.swust-6DL.2. They accounted for 9.0%-21.3% of the phenotypic variation. Two QTLs, namely, QGWpd.swust-3BS and QGWpd.swust-6DL, were detected for GW on chromosomes 3B and 6D, respectively. These QTLs explained 12.8%-14.6% and 10.8%-15.2% of the phenotypic variation, respectively. In addition, two QTLs, i.e., QLWRpd.swust-7AS.1 and QLWRpd.swust-7AS.2, were detected on chromosome 7A for the grain LWR, which explained 10.9%-11.6% and 11.6%-11.2% of the phenotypic variation, respectively. Another QTL, named QGNSpd-swust-6DS, was discovered on chromosome 6D, which determines the GNS and which accounted for 11.4%-13.8% of the phenotypic variation. Furthermore, five QTLs associated with PH were mapped on chromosomes 2D, 3A, 5A, 6B, and 7B. These QTLs were QPHpd.swust-2DL, QPHpd.swust-3AL, QPHpd.swust-5AL, QPHpd.swust-6BL, and QPHpd.swust-7BS, which accounted for 11.3%-19.3% of the phenotypic variation. Lastly, a QTL named QSLpd.swust-3AL, conferring SL, was detected on chromosome 3A and explained 16.1%-17.6% of the phenotypic variation. All of these QTLs were defined within the physical interval of the Chinese spring reference genome.

Discussion

The findings of this study have significant implications for the development of fine genetic maps, for genomic breeding, and for marker-assisted selection to enhance wheat grain yield.

Combining GWAS and comparative genomics to fine map candidate genes for days to flowering in mung bean

BACKGROUND

Mung bean (Vigna radiata (L.) Wilczek), is an important pulse crop in the global south. Early flowering and maturation are advantageous traits for adaptation to northern and southern latitudes. This study investigates the genetic basis of the Days-to-Flowering trait (DTF) in mung bean, combining genome-wide association studies (GWAS) in mung bean and comparisons with orthologous genes involved with control of DTF responses in soybean (Glycine max (L) Merr) and Arabidopsis (Arabidopsis thaliana).

RESULTS

The most significant associations for DTF were on mung bean chromosomes 1, 2, and 4. Only the SNPs on chromosomes 1 and 4 were heavily investigated using downstream analysis. The chromosome 1 DTF association is tightly linked with a cluster of locally duplicated FERONIA (FER) receptor-like protein kinase genes, and the SNP occurs within one of the FERONIA genes. In Arabidopsis, an orthologous FERONIA gene (AT3G51550), has been reported to regulate the expression of the FLOWERING LOCUS C (FLC). For the chromosome 4 DTF locus, the strongest candidates are Vradi04g00002773 and Vradi04g00002778, orthologous to the Arabidopsis PhyA and PIF3 genes, encoding phytochrome A (a photoreceptor protein sensitive to red to far-red light) and phytochrome-interacting factor 3, respectively. The soybean PhyA orthologs include the classical loci E3 and E4 (genes GmPhyA3, Glyma.19G224200, and GmPhyA2, Glyma.20G090000). The mung bean PhyA ortholog has been previously reported as a candidate for DTF in studies conducted in South Korea.

CONCLUSION

The top two identified SNPs accounted for a significant proportion (~ 65%) of the phenotypic variability in mung bean DTF by the six significant SNPs (39.61%), with a broad-sense heritability of 0.93. The strong associations of DTF with genes that have orthologs with analogous functions in soybean and Arabidopsis provide strong circumstantial evidence that these genes are causal for this trait. The three reported loci and candidate genes provide useful targets for marker-assisted breeding in mung beans.

Complex plant responses to drought and heat stress under climate change

Global climate change is predicted to result in increased yield losses of agricultural crops caused by environmental conditions. In particular, heat and drought stress are major factors that negatively affect plant development and reproduction, and previous studies have revealed how these stresses induce plant responses at physiological and molecular levels. Here, we provide a comprehensive overview of current knowledge concerning how drought, heat, and combinations of these stress conditions affect the status of plants, including crops, by affecting factors such as stomatal conductance, photosynthetic activity, cellular oxidative conditions, metabolomic profiles, and molecular signaling mechanisms. We further discuss stress-responsive regulatory factors such as transcription factors and signaling factors, which play critical roles in adaptation to both drought and heat stress conditions and potentially function as 'hubs' in drought and/or heat stress responses. Additionally, we present recent findings based on forward genetic approaches that reveal natural variations in agricultural crops that play critical roles in agricultural traits under drought and/or heat conditions. Finally, we provide an overview of the application of decades of study results to actual agricultural fields as a strategy to increase drought and/or heat stress tolerance. This review summarizes our current understanding of plant responses to drought, heat, and combinations of these stress conditions.

Genome-wide association mapping for pre-harvest sprouting in European winter wheat detects novel resistance QTL, pleiotropic effects, and structural variation in multiple genomes

Pre-harvest sprouting (PHS), germination of seeds before harvest, is a major problem in global wheat (Triticum aestivum L.) production, and leads to reduced bread-making quality in affected grain. Breeding for PHS resistance can prevent losses under adverse conditions. Selecting resistant lines in years lacking pre-harvest rain, requires challenging of plants in the field or in the laboratory or using genetic markers. Despite the availability of a wheat reference and pan-genome, linking markers, genes, allelic, and structural variation, a complete understanding of the mechanisms underlying various sources of PHS resistance is still lacking. Therefore, we challenged a population of European wheat varieties and breeding lines with PHS conditions and phenotyped them for PHS traits, grain quality, phenological and agronomic traits to conduct genome-wide association mapping. Furthermore, we compared these marker-trait associations to previously reported PHS loci and evaluated their usefulness for breeding. We found markers associated with PHS on all chromosomes, with strong evidence for novel quantitative trait locus/loci (QTL) on chromosome 1A and 5B. The QTL on chromosome 1A lacks pleiotropic effect, for the QTL on 5B we detected pleiotropic effects on phenology and grain quality. Multiple peaks on chromosome 4A co-located with the major resistance locus Phs-A1, for which two causal genes, TaPM19 and TaMKK3, have been proposed. Mapping markers and genes to the pan-genome and chromosomal alignments provide evidence for structural variation around this major PHS-resistance locus. Although PHS is controlled by many loci distributed across the wheat genome, Phs-A1 on chromosome 4A seems to be the most effective and widely deployed source of resistance, in European wheat varieties.

Revolutionizing nematode management to achieve global food security goals - An overview

Nematodes are soil-dwelling organisms that inflict substantial damage to crops, resulting in significant declines in agricultural productivity. Consequently, they are recognized as one of the primary contributors to global crop damage, with profound implications for food security. Nematology research assumes a pivotal role in tackling this issue and safeguarding food security. The pursuit of nematology research focused on mitigating nematode-induced crop damage and promoting sustainable agriculture represents a fundamental strategy for enhancing food security. Investment in nematology research is crucial to advance food security objectives by identifying and managing nematode species, developing novel technologies, comprehending nematode ecology, and strengthening the capabilities of researchers and farmers. This endeavor constitutes an indispensable step toward addressing one of the most pressing challenges in achieving global food security and promoting sustainable agricultural practices. Primarily, research endeavors facilitate the identification of nematode species responsible for crop damage, leading to the development of effective management strategies. These strategies encompass the utilization of resistant crop varieties, implementation of cultural practices, biological control, and chemical interventions. Secondly, research efforts contribute to the development of innovative technologies aimed at managing nematode populations, such as gene editing techniques that confer resistance to nematode infestations in crops. Additionally, the exploration of beneficial microbes, such as certain fungi and bacteria, as potential biocontrol agents against nematodes, holds promise. The study of nematode ecology represents a foundational research domain that fosters a deeper comprehension of nematode biology and ecological interactions. This knowledge is instrumental in devising precise and efficacious management strategies.

CRISPR-Cas9 based molecular breeding in crop plants: a review

Traditional crop breeding techniques are not quickly boosting yields to fulfill the expanding population needs. Long crop lifespans hinder the ability of plant breeding to develop superior crop varieties. Due to the arduous crossing, selecting, and challenging processes, it can take decades to establish new varieties with desired agronomic traits. Develop new plant varieties instantly to reduce hunger and improve food security. As a result of the adoption of conventional agricultural techniques, crop genetic diversity has decreased over time. Several traditional and molecular techniques, such as genetic selection, mutant breeding, somaclonal variation, genome-wide association studies, and others, have improved agronomic traits associated with agricultural plant productivity, quality, and resistance to biotic and abiotic stresses. In addition, modern genome editing approaches based on programmable nucleases, CRISPR, and Cas9 proteins have escorted an exciting new era of plant breeding. Plant breeders and scientists worldwide rely on cutting-edge techniques like quick breeding, genome editing tools, and high-throughput phenotyping to boost crop breeding output. This review compiles discoveries in numerous areas of crop breeding, such as using genome editing tools to accelerate the breeding process and create yearly crop generations with the desired features, to describe the shift from conventional to modern plant breeding techniques.

Genomic prediction for root and yield traits of barley under a water availability gradient: a case study comparing different spatial adjustments

BACKGROUND

In drought periods, water use efficiency depends on the capacity of roots to extract water from deep soil. A semi-field phenotyping facility (RadiMax) was used to investigate above-ground and root traits in spring barley when grown under a water availability gradient. Above-ground traits included grain yield, grain protein concentration, grain nitrogen removal, and thousand kernel weight. Root traits were obtained through digital images measuring the root length at different depths. Two nearest-neighbor adjustments (M1 and M2) to model spatial variation were used for genetic parameter estimation and genomic prediction (GP). M1 and M2 used (co)variance structures and differed in the distance function to calculate between-neighbor correlations. M2 was the most developed adjustment, as accounted by the Euclidean distance between neighbors.

RESULTS

The estimated heritabilities ([Formula: see text]) ranged from low to medium for root and above-ground traits. The genetic coefficient of variation ([Formula: see text]) ranged from 3.2 to 7.0% for above-ground and 4.7 to 10.4% for root traits, indicating good breeding potential for the measured traits. The highest [Formula: see text] observed for root traits revealed that significant genetic change in root development can be achieved through selection. We studied the genotype-by-water availability interaction, but no relevant interaction effects were detected. GP was assessed using leave-one-line-out (LOO) cross-validation. The predictive ability (PA) estimated as the correlation between phenotypes corrected by fixed effects and genomic estimated breeding values ranged from 0.33 to 0.49 for above-ground and 0.15 to 0.27 for root traits, and no substantial variance inflation in predicted genetic effects was observed. Significant differences in PA were observed in favor of M2.

CONCLUSIONS

The significant [Formula: see text] and the accurate prediction of breeding values for above-ground and root traits revealed that developing genetically superior barley lines with improved root systems is possible. In addition, we found significant spatial variation in the experiment, highlighting the relevance of correctly accounting for spatial effects in statistical models. In this sense, the proposed nearest-neighbor adjustments are flexible approaches in terms of assumptions that can be useful for semi-field or field experiments.

Genomic regions of durum wheat involved in water productivity

Durum wheat is a staple food in the Mediterranean Basin, mostly cultivated under rainfed conditions. As such, the crop is often exposed to moisture stress. Therefore, the identification of genetic factors controlling the capacity of genotypes to convert moisture into grain yield (i.e., water productivity) is quintessential to stabilize production despite climatic variations. A global panel of 384 accessions was tested across 18 Mediterranean environments (in Morocco, Lebanon, and Jordan) representing a vast range of moisture levels. The accessions were assigned to water responsiveness classes, with genotypes 'Responsive to Low Moisture' reaching an average +1.5 kg ha-1 mm-1 yield advantage. Genome wide association studies revealed that six loci explained most of this variation. A second validation panel tested under moisture stress confirmed that carrying the positive allele at three loci on chromosomes 1B, 2A, and 7B generated an average water productivity gain of +2.2 kg ha-1 mm-1. These three loci were tagged by kompetitive allele specific PCR (KASP) markers, and these were used to screen a third independent validation panel composed of elites tested across moisture stressed sites. The three KASP combined predicted up to 10% of the variation for grain yield at 60% accuracy. These loci are now ready for molecular pyramiding and transfer across cultivars to improve the moisture conversion of durum wheat.

A SNP variation in the Sucrose synthase (SoSUS) gene associated with sugar-related traits in sugarcane

Background

Sugarcane (Saccharum spp.) is an economically significant crop for both the sugar and biofuel industries. Breeding sugarcane cultivars with high-performance agronomic traits is the most effective approach for meeting the rising demand for sugar and biofuels. Molecular markers associated with relevant agronomic traits could drastically reduce the time and resources required to develop new sugarcane varieties. Previous sugarcane candidate gene association analyses have found single nucleotide polymorphism (SNP) markers associated with sugar-related traits. This study aims to validate these associated SNP markers of six genes, including Lesion simulating disease 1 (LSD), Calreticulin (CALR), Sucrose synthase 1 (SUS1), DEAD-box ATP-dependent RNA helicase (RH), KANADI1 (KAN1), and Sodium/hydrogen exchanger 7 (NHX7), in a diverse population in 2-year and two-location evaluations.

Methods

After genotyping of seven targeted SNP markers was performed by PCR Allelic Competitive Extension (PACE) SNP genotyping, the association with sugar-related traits and important cane yield component traits was determined on a set of 159 sugarcane genotypes. The marker-trait relationships were validated and identified by both t-test analysis and an association analysis based on the general linear model.

Results

The mSoSUS1_SNPCh10.T/C and mSoKAN1_SNPCh7.T/C markers that were designed from the SUS1 and KAN1 genes, respectively, showed significant associations with different amounts of sugar-related traits and yield components. The mSoSUS1_SNPCh10.T/C marker was found to have more significant association with sugar-related traits, including pol, CCS, brix, fiber and sugar yield, with p values of 6.08 × 10-6 to 4.35 × 10-2, as well as some cane yield component traits with p values of 1.61 × 10-4 to 3.35 × 10-2. The significant association is consistent across four environments.

Conclusion

Sucrose synthase (SUS) is considered a crucial enzyme involved in sucrose metabolism. This marker is a high potential functional marker that may be used in sugarcane breeding programs to select superior sugarcane with good fiber and high sugar contents.

Identification of QTLs and allelic effect controlling lignan content in sesame (Sesamum indicum L.) using QTL-seq approach

Sesame (Sesamum indicum L.), an oilseed crop, is gaining worldwide recognition for its healthy functional ingredients as consumption increases. The content of lignans, known for their antioxidant and anti-inflammatory effects, is a key agronomic trait that determines the industrialization of sesame. However, the study of the genetics and physiology of lignans in sesame is challenging, as they are influenced by multiple genes and environmental factors, therefore, the understanding of gene function and synthetic pathways related to lignan in sesame is still limited. To address these knowledge gaps, we conducted genetic analyses using F7 recombinant inbred line (RIL) populations derived from Goenbaek and Gomazou as low and high lignin content variants, respectively. Using the QTL-seq approach, we identified three loci, qLignan1-1, qLignan6-1, and qLignan11-1, that control lignan content, specifically sesamin and sesamolin. The allelic effect between loci was evaluated using the RIL population. qLignan6-1 had an additive effect that increased lignan content when combined with the other two loci, suggesting that it could be an important factor in gene pyramiding for the development of high-lignan varieties. This study not only highlights the value of sesame lignan, but also provides valuable insights for the development of high-lignan varieties through the use of DNA markers in breeding strategies. Overall, this research contributes to our understanding of the importance of sesame oil and facilitates progress in sesame breeding for improved lignan content.

Multi-locus genome-wide association study and genomic prediction for flowering time in chrysanthemum

MAIN CONCLUSION

Multi-locus GWAS detected several known and candidate genes responsible for flowering time in chrysanthemum. The associations could greatly increase the predictive ability of genome selection that accelerates the possible application of GS in chrysanthemum breeding. Timely flowering is critical for successful reproduction and determines the economic value for ornamental plants. To investigate the genetic architecture of flowering time in chrysanthemum, a multi-locus genome-wide association study (GWAS) was performed using a collection of 200 accessions and 330,710 single-nucleotide polymorphisms (SNPs) via 3VmrMLM method. Five flowering time traits including budding (FBD), visible colouring (VC), early opening (EO), full-bloom (OF) and senescing (SF) stages, plus five derived conditional traits were recorded in two environments. Extensive phenotypic variations were observed for these flowering time traits with coefficients of variation ranging from 6.42 to 38.27%, and their broad-sense heritability ranged from 71.47 to 96.78%. GWAS revealed 88 stable quantitative trait nucleotides (QTNs) and 93 QTN-by-environment interactions (QEIs) associated with flowering time traits, accounting for 0.50-8.01% and 0.30-10.42% of the phenotypic variation, respectively. Amongst the genes around these stable QTNs and QEIs, 21 and 10 were homologous to known flowering genes in Arabidopsis; 20 and 11 candidate genes were mined by combining the functional annotation and transcriptomics data, respectively, such as MYB55, FRIGIDA-like, WRKY75 and ANT. Furthermore, genomic selection (GS) was assessed using three models and seven unique marker datasets. We found the prediction accuracy (PA) using significant SNPs identified by GWAS under SVM model exhibited the best performance with PA ranging from 0.90 to 0.95. Our findings provide new insights into the dynamic genetic architecture of flowering time and the identified significant SNPs and candidate genes will accelerate the future molecular improvement of chrysanthemum.

Meta-QTL s and haplotypes for efficient zinc biofortification of rice

Biofortification of rice with improved grain zinc (Zn) content is the most sustainable and cost-effective approach to address Zn malnutrition in Asia. Genomics-assisted breeding using precise and consistent Zn quantitative trait loci (QTLs), genes, and haplotypes can fast-track the development of Zn biofortified rice varieties. We conducted the meta-analysis of 155 Zn QTLs reported from 26 different studies. Results revealed 57 meta-QTLs with a significant reduction of 63.2% and 80% in the number and confidence interval of the Zn QTLs, respectively. Meta-quantitative trait loci (MQTLs) regions were found to be enriched with diverse metal homeostasis genes; at least 11 MQTLs were colocated with 20 known major genes involved in the production of root exudates, metal uptake, transport, partitioning, and loading into grains in rice. These genes were differentially expressed in vegetative and reproductive tissues, and a complex web of interactions were observed among them. We identified superior haplotypes and their combinations for nine candidate genes (CGs), and the frequency and allelic effects of superior haplotypes varied in different subgroups. The precise MQTLs with high phenotypic variance, CGs, and superior haplotypes identified in our study are useful for an efficient Zn biofortification of rice and to ensure Zn as an essential component of all the future rice varieties through mainstreaming of Zn breeding.

Investigation of the association between goat DNMT3B gene polymorphism and growth traits

The DNA methyltransferase 3 beta (DNMT3B) gene is key for DNA methylation and has been well recognized in regulating growth and development. A previous observation indicated that an 11-bp indel of DNMT3B affected the reproductive traits in goats, yet the effect of this polymorphism on body measurement traits in goats has not been reported. This study aims to investigate the associations between DNMT3B gene polymorphism and goat growth traits. We investigated this 11-bp indel in 2184 goats and three genotypes have been found in Shaanbei white cashmere goat (SBWC): insertion/insertion (II), deletion/deletion (DD) and insertion/deletion (ID). Only ID and DD genotypes were detected in Nubian goats and Guizhou heima goat (GZHM). The allele frequencies analyzed revealed that the 'D' allele frequencies were higher in all three goat breeds. Further association analysis demonstrated that this indel is markedly associated with the cannon circumference (CC) and cannon circumference index (CCI) of SBWC and cannon circumference (CC) of Nubian goats (p < .05). The CC and CCI are essential indicators to measure the growth status of goats. In summary, our study sheds some light on the potential impact of the 11-bp indel polymorphism of the DNMT3B gene on improving the growth traits in goats.

Polymorphism within the GATA binding protein 4 gene is significantly associated with goat litter size

GATA binding protein 4 (GATA4) is a typical transcription binding factor, and its main functions include regulating the proliferation, differentiation and apoptosis of ovarian granulosa cells, promoting spermatogenesis and sex differentiation, implying that this gene have possibly roles in animal reproduction. This study aims to detect five potential insertion/deletions (indels) of the GATA4 gene in 606 healthy unrelated Shaanbei white cashmere (SBWC) goats and analyze its association with the litter size. The electrophoresis and DNA sequencing identified two polymorphic indels (e.g., P4-Del-8bp and P5-Ins-9bp indel). Then T-test analysis showed that P4-Del-8bp was significantly correlated with litter size (p = 0.022) because of two different genotypes detected, e.g., insertion-deletion (ID) and deletion-deletion (DD), and the average litter size of individuals with DD genotype goats was higher than that of others. However, there was no correlation between P5-Ins-9bp and lambing of goats. Chi-square (X2) test found that the distribution of and P4-Del-8bp genotypes (X2 = 6.475, p = 0.011) was significantly different between single and multiple-lamb groups, while P5-Ins-9bp (X2 = 0.030, p = 0.862) was not. Therefore, these findings revealed that P4-Del-8bp polymorphism of goat GATA4 gene was a potential molecular marker significantly associated with litter size, which can be used for the marker-assisted selection (MAS) breeding to improve goat industry.

CRISPR-mediated acceleration of wheat improvement: advances and perspectives

Common wheat (Triticum aestivum) is one of the most widely cultivated and consumed crops globally. In the face of limited arable land and climate changes, it is a great challenge to maintain current and increase future wheat production. Enhancing agronomic traits in wheat by introducing mutations across all three homoeologous copies of each gene has proven to be a difficult task due to its large genome with high repetition. However, clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease (Cas) genome editing technologies offer a powerful means of precisely manipulating the genomes of crop species, thereby opening up new possibilities for biotechnology and breeding. In this review, we first focus on the development and optimization of the current CRISPR-based genome editing tools in wheat, emphasizing recent breakthroughs in precise and multiplex genome editing. We then describe the general procedure of wheat genome editing and highlight different methods to deliver the genome editing reagents into wheat cells. Furthermore, we summarize the recent applications and advancements of CRISPR/Cas technologies for wheat improvement. Lastly, we discuss the remaining challenges specific to wheat genome editing and its future prospects.

Pyramiding resistance genes for bacterial leaf blight (Xanthomonas oryzae pv. Oryzae) into the popular rice variety, Pratikshya through marker assisted backcrossing

BACKGROUND

Bacterial leaf blight (BLB) is one of the major biotic stress in rice cultivation. Management techniques, such as the development of BLB-resistant cultivars, are required to lessen the severity of the disease attack and yield losses. Pratikshya was selected in the present investigation as the recipient parent, as it is one of the popular high-yielding rice varieties of Odisha, India, which is having excellent grain as well as cooking quality. However, Pratikshya is highly susceptible to BLB which is prevalent in Eastern Indian region.

METHODS AND RESULTS

Three major BLB resistance genes xa5, xa13, and Xa21 from the donor source Swarna MAS (CR Dhan 800) were attempted to introduce into Pratikshya through a marker-assisted backcross breeding program. Those markers closely linked to the target genes were employed for foreground selection in the segregating generations till BC2F3. In each backcross generation, progenies containing all three targeted resistance genes and phenotypically more similar to the recipient parent, Pratikshya were selected and backcrossed. Screening of 1,598 plants of the BC2F2 population was conducted against BLB using Xoo inoculum and 35 resistant plants similar to Pratikshya were carried forward to the next generation. In the BC2F3 generation, 31 plants were found to possess all the three resistance genes. For background selection of plants carrying resistance genes 45 polymorphic SSR markers were employed. Evaluation of the pyramided lines at BC2F4 generation exhibited that, most pyramided lines were similar to Pratikshya in terms of morphological features and yield parameters, and some lines were superior to the recurrent parent in terms of morphological features and yield parameters.

CONCLUSION

The three-gene pyramided lines showed a high level of resistance to BLB infection and are anticipated to offer a significant yield advantage over the recipient parent Pratikshya. The pyramided lines can further be used for multi-location trial, so as to be released as a variety or can be used as a potential donor for BLB resistance genes.

QTL Verification and Candidate Gene Screening of Fiber Quality and Lint Percentage in the Secondary Segregating Population of Gossypium hirsutum

Fiber quality traits, especially fiber strength, length, and micronaire (FS, FL, and FM), have been recognized as critical fiber attributes in the textile industry, while the lint percentage (LP) was an important indicator to evaluate the cotton lint yield. So far, the genetic mechanism behind the formation of these traits is still unclear. Quantitative trait loci (QTL) identification and candidate gene validation provide an effective methodology to uncover the genetic and molecular basis of FL, FS, FM, and LP. A previous study identified three important QTL/QTL cluster loci, harboring at least one of the above traits on chromosomes A01, A07, and D12 via a recombinant inbred line (RIL) population derived from a cross of Lumianyan28 (L28) × Xinluzao24 (X24). A secondary segregating population (F2) was developed from a cross between L28 and an RIL, RIL40 (L28 × RIL40). Based on the population, genetic linkage maps of the previous QTL cluster intervals on A01 (6.70-10.15 Mb), A07 (85.48-93.43 Mb), and D12 (0.40-1.43 Mb) were constructed, which span 12.25, 15.90, and 5.56 cM, with 2, 14, and 4 simple sequence repeat (SSR) and insertion/deletion (Indel) markers, respectively. QTLs of FL, FS, FM, and LP on these three intervals were verified by composite interval mapping (CIM) using WinQTL Cartographer 2.5 software via phenotyping of F2 and its derived F2:3 populations. The results validated the previous primary QTL identification of FL, FS, FM, and LP. Analysis of the RNA-seq data of the developing fibers of L28 and RIL40 at 10, 20, and 30 days post anthesis (DPA) identified seven differentially expressed genes (DEGs) as potential candidate genes. qRT-PCR verified that five of them were consistent with the RNA-seq result. These genes may be involved in regulating fiber development, leading to the formation of FL, FS, FM, and LP. This study provides an experimental foundation for further exploration of these functional genes to dissect the genetic mechanism of cotton fiber development.

Breeding Cultivars for Resistance to the African Sweetpotato Weevils, Cylas puncticollis and Cylas brunneus, in Uganda: A Review of the Current Progress

In sub-Saharan Africa, sweetpotato weevils are the major pests of cultivated sweetpotato, causing estimated losses of between 60% and 100%, primarily during dry spells. The predominantly cryptic feeding behavior of Cylas spp. within their roots makes their control difficult, thus, host plant resistance is one of the most promising lines of protection against these pests. However, limited progress has been made in cultivar breeding for weevil resistance, partly due to the complex hexaploid genome of sweetpotato, which complicates conventional breeding, in addition to the limited number of genotypes with significant levels of resistance for use as sources of resistance. Pollen sterility, cross incompatibility, and poor seed set and germination in sweetpotato are also common challenges in improving weevil resistance. The accurate phenotyping of sweetpotato weevil resistance to enhance the efficiency of selection has been equally difficult. Genomics-assisted breeding, though in its infancy stages in sweetpotato, has a potential application in overcoming some of these barriers. However, it will require the development of more genomic infrastructure, particularly single-nucleotide polymorphism markers (SNPs) and robust next-generation sequencing platforms, together with relevant statistical procedures for analyses. With the recent advances in genomics, we anticipate that genomic breeding for sweetpotato weevil resistance will be expedited in the coming years. This review sheds light on Uganda's efforts, to date, to breed against the Cylas puncticollis (Boheman) and Cylas brunneus (Fabricius) species of African sweetpotato weevil.

The Potential Genetic Effect for Yield and Foliar Disease Resistance in Faba Bean (Vicia faba L.) Assessed via Morphological and SCoT Markers

Faba bean is considered one of the most prominent grain legumes, with high protein content for human food consumption and livestock feed. The present study evaluated the nature of gene action and determined the genetic diversity among different populations of three crosses for resistance to foliar diseases at the molecular level. Analysis of variance exposed significant differences among the generations for all measured traits. Both dominance and additive gene effects were essential, but dominance genes, for the most part, exhibited greater effects than additive ones. This indicates an essential role for dominant genes alongside the additives one in inheriting such traits. The third cross (Marina × Giza 40) gave desired significant and positive (additive × additive) values for the number of pods/plant, seeds/plant, and seed yield/plant, in addition to desirable negative values for chocolate spot and rust characteristics. Furthermore, assessing the lines under study using seven SCoT primers disclosed three bands with recorded molecular weights of 260, 207, and 178 bp, generated by SCoT-1, SCoT-4, and SCoT-7 primers, respectively. These bands exist in the resistant parent (Marina), which could be attributed to the high-disease-resistance phenotypes, and they are absent in the sensitive parent (Giza 40) and other putative sensitive lines. Based on the molecular profiles and the genetic similarity between parents and the selected lines, the highest similarity value (0.91) was detected between Marina genotype and BC1, revealing a high foliar disease resistance. Meanwhile, Giza 40 (susceptible to foliar diseases) exhibited the maximum value (0.93) with F2. Additionally, cluster analysis based on genetic relationships was performed, and a high level of correlation between the results of PCR-based SCoT analysis and the foliar disease reactions was observed in the field. Consequently, this study concluded that SCoT markers created reliable banding profiles for evaluating genetic polymorphism among faba bean lines, which could be a foundation for developing an efficient breeding program.

Crop/Plant Modeling Supports Plant Breeding: I. Optimization of Environmental Factors in Accelerating Crop Growth and Development for Speed Breeding

The environmental conditions in customered speed breeding practice are, to some extent, empirical and, thus, can be further optimized. Crop and plant models have been developed as powerful tools in predicting growth and development under various environments for extensive crop species. To improve speed breeding, crop models can be used to predict the phenotypes resulted from genotype by environment by management at the population level, while plant models can be used to examine 3-dimensional plant architectural development by microenvironments at the organ level. By justifying the simulations via numerous virtual trials using models in testing genotype × environment × management, an optimized combination of environmental factors in achieving desired plant phenotypes can be quickly determined. Artificial intelligence in assisting for optimization is also discussed. We admit that the appropriate modifications on modeling algorithms or adding new modules may be necessary in optimizing speed breeding for specific uses. Overall, this review demonstrates that crop and plant models are promising tools in providing the optimized combinations of environment factors in advancing crop growth and development for speed breeding.

Adapting crop production to climate change and air pollution at different scales

Air pollution and climate change are tightly interconnected and jointly affect field crop production and agroecosystem health. Although our understanding of the individual and combined impacts of air pollution and climate change factors is improving, the adaptation of crop production to concurrent air pollution and climate change remains challenging to resolve. Here we evaluate recent advances in the adaptation of crop production to climate change and air pollution at the plant, field and ecosystem scales. The main approaches at the plant level include the integration of genetic variation, molecular breeding and phenotyping. Field-level techniques include optimizing cultivation practices, promoting mixed cropping and diversification, and applying technologies such as antiozonants, nanotechnology and robot-assisted farming. Plant- and field-level techniques would be further facilitated by enhancing soil resilience, incorporating precision agriculture and modifying the hydrology and microclimate of agricultural landscapes at the ecosystem level. Strategies and opportunities for crop production under climate change and air pollution are discussed.

Genome-wide survey and characterization of microsatellites in cashew and design of a web-based microsatellite database: CMDB

The cashew is an edible tree nut crop having a wide range of food and industrial applications. Despite great economic importance, the genome-wide characterization of microsatellites [simple sequence repeats (SSRs)] in cashew is lacking. In this study, we carried out the first comprehensive genome-wide microsatellites/SSRs characterization in cashew and developed polymorphic markers and a web-based microsatellite database. A total of 54526 SSRs were discovered in the cashew genome, with a mean frequency of 153 SSRs/Mb. Among the mined genome-wide SSRs (2-6 bp size motifs), the dinucleotide repeat motifs were dominant (68.98%) followed by the trinucleotides (24.56%). The Class I type of SSRs (≥20 bp) were 45.10%, while Class II repeat motifs (≥12-<20 bp) were 54.89% of the total genomic SSRs discovered here. Further, the AT-rich SSRs occurred more frequently in the cashew genome (84%) compared to the GC-rich SSRs. The validation of the in silico-mined genome-wide SSRs by PCR screening in cashew genotypes resulted in the development of 59 polymorphic SSR markers, and the polymorphism information content (PIC) of the polymorphic SSR markers ranged from 0.19 to 0.84. Further, a web-based database, "Cashew Microsatellite Database (CMDB)," was constructed to provide access to the genome-wide SSRs mined in this study as well as transcriptome-based SSRs from our previous study to the research community through a user-friendly searchable interface. Besides, CMDB provides information on experimentally validated SSRs. CMDB permits the retrieval of SSR markers information with the customized search options. Altogether, the genome-wide SSRs characterization, the polymorphic markers and CMDB database developed in this study would serve as valuable marker resources for DNA fingerprinting, germplasm characterization, genetic studies, and molecular breeding in cashew and related Anacardium species.

A meta-QTL analysis highlights genomic hotspots associated with phosphorus use efficiency in rice (Oryza sativa L.)

Phosphorus use efficiency (PUE) is a complex trait, governed by many minor quantitative trait loci (QTLs) with small effects. Advances in molecular marker technology have led to the identification of QTLs underlying PUE. However, their practical use in breeding programs remains challenging due to the unstable effects in different genetic backgrounds and environments, interaction with soil status, and linkage drag. Here, we compiled PUE QTL information from 16 independent studies. A total of 192 QTLs were subjected to meta-QTL (MQTL) analysis and were projected into a high-density SNP consensus map. A total of 60 MQTLs, with significantly reduced number of initial QTLs and confidence intervals (CI), were identified across the rice genome. Candidate gene (CG) mining was carried out for the 38 MQTLs supported by multiple QTLs from at least two independent studies. Genes related to amino and organic acid transport and auxin response were found to be abundant in the MQTLs linked to PUE. CGs were cross validated using a root transcriptome database (RiceXPro) and haplotype analysis. This led to the identification of the eight CGs (OsARF8, OsSPX-MFS3, OsRING141, OsMIOX, HsfC2b, OsFER2, OsWRKY64, and OsYUCCA11) modulating PUE. Potential donors for superior PUE CG haplotypes were identified through haplotype analysis. The distribution of superior haplotypes varied among subspecies being mostly found in indica but were largely scarce in japonica. Our study offers an insight on the complex genetic networks that modulate PUE in rice. The MQTLs, CGs, and superior CG haplotypes identified in our study are useful in the combination of beneficial alleles for PUE in rice.

In Vitro Culture Technology and Advanced Biotechnology Tools Toward Improvement in Gladiolus (Gladiolus species): Present Scenario and Future Prospects

In the world's flower trade, gladiolus (Gladiolus spp.) is ranked first among bulbous flowers and eighth among cut flowers, with more than 30,000 different cultivars being grown. Mass multiplication and commercialization are restricted by the traditional propagation methods. However, the large-scale proliferation and improvement of the gladiolus have been accomplished with the aid of plant tissue culture and other biotechnological techniques. The current review includes a thorough examination of the growth and development parameters required for successful in vitro gladiolus development as well as cormel formation. Moreover, focus is being given to various techniques and methods such as in vitro cytogenetic stability and modification of chromosome number, in vitro mutagenesis and selection of pest resistance, in vitro identification and selection to develop virus-free germplasm, cryopreservation, synthetic seed technology, identifying virus diseases by RT-PCR, somaclonal variation, and protoplast and somatic hybridization. Molecular markers and their applications for genetic diversity analysis, relationships between different genotypes, and clonal stability analysis in Gladiolus species have been conducted by several research groups worldwide and are also being discussed. The article also covers efforts to enhance the functionality of plant phenotypes through genetic transformation. Future prospects for further improvement of ornamental gladiolus are also explored. Overall, the current review provides insight into the applications of basic and advanced biotechnological tools for gladiolus improvement.

Development and Application of a Cleaved Amplified Polymorphic Sequence Marker (Phyto) Linked to the Pc5.1 Locus Conferring Resistance to Phytophthora capsici in Pepper (Capsicum annuum L.)

Phytophthora capsici causes destructive disease in several crop species, including pepper (Capsicum annuum L.). Resistance in this species is physiologically and genetically complex due to many P. capsici virulence phenotypes and different QTLs and R genes among the identified resistance sources. Several primer pairs were designed to follow an SNP (G/A) within the CA_011264 locus linked to the Pc5.1 locus. All primer pairs were designed on DNA sequences derived from CaDMR1, a homoserine kinase (HSK), which is a gene candidate responsible for the major QTL on chromosome P5 for resistance to P. capsici. A panel of 69 pepper genotypes from the Southern Seed germplasm collection was used to screen the primer pairs designed. Of these, two primers (Phyto_for_2 and Phyto_rev_2) surrounding the SNP proved successful in discriminating susceptible and resistant genotypes when combined with a restriction enzyme (BtgI). This new marker (called Phyto) worked as expected in all genotypes tested, proving to be an excellent candidate for marker-assisted selection in breeding programs aimed at introgressing the resistant locus into pure lines.

L. P, Pal D, Sivasamy M, Jain N, Singh GP, Singh PK. Marker-assisted selection for transfer of QTLs to a promising line for drought tolerance in wheat (Triticum aestivum L.)

Wheat crop is subjected to various biotic and abiotic stresses, which affect crop productivity and yield. Among various abiotic stresses, drought stress is a major problem considering the current global climate change scenario. A high-yielding wheat variety, HD3086, has been released for commercial cultivation under timely sown irrigated conditions for the North Western Plain Zone (NWPZ) and North Eastern Plain Zone NEPZ of India. Presently, HD3086 is one of the highest breeder seed indented wheat varieties and has a stable yield over the years. However, under moisture deficit conditions, its potential yield cannot be achieved. The present study was undertaken to transfer drought-tolerant QTLs in the background of the variety HD3086 using marker-assisted backcross breeding. QTLs governing Biomass (BIO), Canopy Temperature (CT), Thousand Kernel Weight (TKW), Normalized Difference Vegetation Index (NDVI), and Yield (YLD) were transferred to improve performance under moisture deficit conditions. In BC1F1, BC2F1, and BC2F2 generations, the foreground selection was carried out to identify the plants with positive QTLs conferring drought tolerance and linked to traits NDVI, CT, TKW, and yield. The positive homozygous lines for targeted QTLs were advanced from BC2F2 to BC2F4 via the pedigree-based phenotypic selection method. Background analysis was carried out in BC2F5 and obtained 78-91% recovery of the recurrent parent genome in the improved lines. Furthermore, the advanced lines were evaluated for 2 years under drought stress to assess improvement in MABB-derived lines. Increased GWPS, TKW, and NDVI and reduced CT was observed in improved lines. Seven improved lines were identified with significantly higher yields in comparison to HD3086 under stress conditions.

A Genomic Evaluation of Six Selected Inbred Lines of the Naturalized Plants of Milk Thistle (Silybum marianum L. Gaertn.) in Korea

Milk thistle (Silybum marianum) belongs to the Asteraceae family and is a medicinal plant native to the Mediterranean Basin. Silymarin in achene is a widely used herbal product for chronic liver disease. There is growing interest in natural medicine using milk thistle in Korea, but the raw material completely relies on imports. Despite its economic importance, phenotypic evaluations of native resources of milk thistle in Korea have not been carried out. In addition, genomic research and molecular marker development are very limited in milk thistle. In this study, we evaluated 220 milk thistle resources consisting of 172 accessions collected from the domestic market, and 48 accessions isolated from 6 accessions distributed by the National Agrobiodiversity Center in Korea. Six plant characteristics (height, seed weight, number of flowers, seed weight per flower, spine length, and color at harvest) were measured, and six samples (M01-M06) were selected to represent the genetic diversity of the population for genomic research. To develop PCR-based and co-dominant insertion/deletion (InDel) markers, we performed genome-wide InDel detection by comparing the whole-genome resequencing data of the six selected accessions with the reference genome sequence (GCA_001541825). As a result, 177 InDel markers with high distinguishability and reproducibility were selected from the 30,845 InDel variants. Unknowingly imported alien plant resources could easily be genetically mixed, and jeopardized seed purity can cause continuous difficulties in the development of high value-added agricultural platforms utilizing natural products. The selected plant materials and 177 validated InDel markers developed via whole-genome resequencing analysis could be valuable resources for breeding, conservation, and ecological studies of natives to Korea, along with acceleration of Silybum marianum industrialization.

Genetic diversity of the breeding collection of tomato varieties in Kazakhstan assessed using SSR, SCAR and CAPS markers

Tomato is one of the most prominent crops in global horticulture and an important vegetable crop in Kazakhstan. The lack of data on the genetic background of local varieties limits the development of tomato breeding in the country. This study aimed to perform an initial evaluation of the breeding collection of tomato varieties from the point of view of their genetic structure and pathogen resistance using a set of PCR based molecular markers, including 13 SSR markers for genetic structure analysis, and 14 SCAR and CAPS markers associated with resistance to five pathogens: three viruses, fungus Fusarium oxysporum, and oomycete P hytophthora infestans. Nine SSR markers were with a PIC value varying from 0.0562 (low information content) to 0.629 (high information content). A weak genetic structure was revealed in the samples of varieties including local cultivars and, predominantly, varieties from Russia and other ex-USSR countries. The local varieties were closely related to several groups of cultivars of Russian origin. Screening for a set of resistance markers revealed the common occurrence of the resistance locus I against Fusarium oxysporum and only the occasional presence of resistance alleles of other markers. No markers of resistance to the three considered viruses were revealed in local tomato varieties. Only two local cultivars had markers of resistance to P. infestans, and only the 'Meruert' cultivar had a combination of resistance markers against P. infestans and F. oxysporum. The obtained results have demonstrated the need for further studies of local tomato varieties with a wider range of molecular markers and source germplasm to lay a foundation for the development of tomato breeding in Kazakhstan.

Mutagenesis-based plant breeding approaches and genome engineering: A review focused on tomato

Breeding is the most important and efficient method for crop improvement involving repeated modification of the genetic makeup of a plant population over many generations. In this review, various accessible breeding approaches, such as conventional breeding and mutation breeding (physical and chemical mutagenesis and insertional mutagenesis), are discussed with respect to the actual impact of research on the economic improvement of tomato agriculture. Tomatoes are among the most economically important fruit crops consumed worldwide because of their high nutritional content and health-related benefits. Additionally, we summarize mutation-based mapping approaches, including Mutmap and MutChromeSeq, for the efficient mapping of several genes identified by random indel mutations that are beneficial for crop improvement. Difficulties and challenges in the adaptation of new genome editing techniques that provide opportunities to demonstrate precise mutations are also addressed. Lastly, this review focuses on various effective and convenient genome editing tools, such as RNA interference (RNAi), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR/Cas9), and their potential for the improvement of numerous desirable traits to allow the development of better varieties of tomato and other horticultural crops.

Rapid and easy construction of a simplified amplicon sequencing (simplified AmpSeq) library for marker-assisted selection

Marker-assisted selection (MAS) is fundamental for plant breeding programs, as it can identify desirable seedlings at a young stage and reduce the cost, time and space needed for plant maintenance, especially for perennial crops. To facilitate the process of genotyping, which is time consuming and laborious, we developed a simplified amplicon sequencing (simplified AmpSeq) library construction method for next-generation sequencing that can be applied to MAS in breeding programs. The method is based on one-step PCR with a mixture of two primer sets: the first consisting of tailed target primers, the second of primers that contain flow-cell binding sites, indexes and tail sequences complementary to those in the first set. To demonstrate the process of MAS using s implified AmpSeq, we created databases of genotypes for important traits by using cultivar collections including triploid cultivars and segregating seedlings of Japanese pear (Pyrus pyrifolia Nakai), Japanese chestnut (Castanea crenata Sieb. et Zucc.) and apple (Malus domestica Borkh.). Simplified AmpSeq has the advantages of high repeatability, ability to estimate allele number in polyploid species and semi-automatic evaluation using target allele frequencies. Because this method provides high flexibility for designing primer sets and targeting any variant, it will be useful for plant breeding programs.

Identification of a Major-Effect Quantitative Trait Loci Associated with Begomovirus Resistance in Cucurbita moschata

Begomoviruses, viz. squash leaf curl China virus and tomato leaf curl New Delhi virus causative diseases are major concerns of quantitative and qualitative losses in pumpkin (Cucurbita moschata) worldwide. Punjab Agricultural University (PAU) in India has identified a resistant source (PVR-1343) against mixed infection (MI-Sq/To) of these begomoviruses. Introgression of resistance in diverse genetic backgrounds requires the identification of quantitative trait loci (QTLs) associated with MI-Sq/To resistance. Phenotyping of 229 F_2:3 progenies derived from the PVR-1343 × P-135 cross revealed digenic recessive inheritance against MI-Sq/To resistance in PVR-1343. To identify the genomic region, resistant and susceptible bulks were subjected to whole-genome resequencing along with their parents. The whole-genome resequence analysis of parents and bulks using QTLseq/QTLseqr approaches identified an overlapping 1.52 Mb region on chromosome 7 (qMI-Sq/To7.1), while chromosomal region spanning 0.87 Mb on chromosome17 (qMI-Sq/To17.1) was additionally identified by QTLseqr. However, the highest peak value on chromosome 7 with three algorithms {G', ∆(SNP-index) and -log₁₀ (P value)} highlighted the major contribution of qMI-Sq/To7.1 in MI-Sq/To resistance. Nine polymorphic SNPs identified within the highly significant qMI-Sq/To7.1 region were converted into KASP markers. KASP genotyping of F₂ individuals narrowed down the qMI-Sq/To7.1 interval to 103 kb region flanked by two markers, Cmo3914729 and Cmo4018182, which contained 16 annotated genes and accounted for 59.84% of phenotypic variation. The Cmo4018182 KASP marker accurately predicted disease reaction in 91% of diverse Cucurbita genotypes and showed nonsynonym substitutions in the coding region of putative candidate SYNTAXIN-121 gene. These findings pave the way for marker-assisted breeding and elucidating the underlying mechanism of begomovirus resistance in C. moschata.

Construction of a genetic linkage map and QTL mapping of fruit quality traits in guava (Psidium guajava L.)

Guava (Psidium guajava L.) is an important fruit crop of the Indian sub-continent, with potential for improvements in quality and yield. The goal of the present study was to construct a genetic linkage map in an intraspecific cross between the elite cultivar 'Allahabad Safeda' and the Purple Guava landrace to identify the genomic regions responsible for important fruit quality traits, viz., total soluble solids, titratable acidity, vitamin C, and sugars. This population was phenotyped in field trials (as a winter crop) for three consecutive years, and showed moderate-to-high values of heterogeneity coefficients along with higher heritability (60.0%-97.0%) and genetic-advance-over-mean values (13.23%-31.17%), suggesting minimal environmental influence on the expression of fruit-quality traits and indicating that these traits can be improved by phenotypic selection methods. Significant correlations and strong associations were also detected among fruit physico-chemical traits in segregating progeny. The constructed linkage map consisted of 195 markers distributed across 11 chromosomes, spanning a length of 1,604.47 cM (average inter-loci distance of 8.80 markers) and with 88.00% coverage of the guava genome. Fifty-eight quantitative trait loci (QTLs) were detected in three environments with best linear unbiased prediction (BLUP) values using the composite interval mapping algorithm of the BIP (biparental populations) module. The QTLs were distributed on seven different chromosomes, explaining 10.95%-17.77% of phenotypic variance, with the highest LOD score being 5.96 for qTSS.AS.pau-6.2. Thirteen QTLs detected across multiple environments with BLUPs indicate stability and utility in a future breeding program for guava. Furthermore, seven QTL clusters with stable or common individual QTLs affecting two or more different traits were located on six linkage groups (LGs), explaining the correlation among fruit-quality traits. Thus, the multiple environmental evaluations conducted here have increased our understanding of the molecular basis of phenotypic variation, providing the basis for future high-resolution fine-mapping and paving the way for marker-assisted breeding of fruit-quality traits.

geneHapR: an R package for gene haplotypic statistics and visualization

BACKGROUND

Together with application of next-generation sequencing technologies and increased accumulation of genomic variation data in different organism species, an opportunity for effectively identification of superior alleles of functional genes to facilitate marker-assisted selection is emerging, and the clarification of haplotypes of functional genes is becoming an essential target in recent study works.

RESULTS

In this paper, we describe an R package 'geneHapR' developed for haplotypes identification, statistics and visualization analysis of candidate genes. This package could integrate genotype data, genomic annotating information and phenotypic variation data to clarify genotype variations, evolutionary-ship, and morphological effects among haplotypes through variants visualization, network construction and phenotypic comparison. 'geneHapR' also provides functions for Linkage Disequilibrium block analysis and visualizing of haplotypes geo-distribution.

CONCLUSIONS

The R package 'geneHapR' provided an easy-to-use tool for haplotype identification, statistic and visualization for candidate gene and will provide useful clues for gene functional dissection and molecular-assistant pyramiding of beneficial alleles of functional locus in future breeding programs.

CRISPR-Based Genome Editing Tools: An Accelerator in Crop Breeding for a Changing Future

Genome editing is an important strategy to maintain global food security and achieve sustainable agricultural development. Among all genome editing tools, CRISPR-Cas is currently the most prevalent and offers the most promise. In this review, we summarize the development of CRISPR-Cas systems, outline their classification and distinctive features, delineate their natural mechanisms in plant genome editing and exemplify the applications in plant research. Both classical and recently discovered CRISPR-Cas systems are included, detailing the class, type, structures and functions of each. We conclude by highlighting the challenges that come with CRISPR-Cas and offer suggestions on how to tackle them. We believe the gene editing toolbox will be greatly enriched, providing new avenues for a more efficient and precise breeding of climate-resilient crops.

Intelligent reprogramming of wheat for enhancement of fungal and nematode disease resistance using advanced molecular techniques

Wheat (Triticum aestivum L.) diseases are major factors responsible for substantial yield losses worldwide, which affect global food security. For a long time, plant breeders have been struggling to improve wheat resistance against major diseases by selection and conventional breeding techniques. Therefore, this review was conducted to shed light on various gaps in the available literature and to reveal the most promising criteria for disease resistance in wheat. However, novel techniques for molecular breeding in the past few decades have been very fruitful for developing broad-spectrum disease resistance and other important traits in wheat. Many types of molecular markers such as SCAR, RAPD, SSR, SSLP, RFLP, SNP, and DArT, etc., have been reported for resistance against wheat pathogens. This article summarizes various insightful molecular markers involved in wheat improvement for resistance to major diseases through diverse breeding programs. Moreover, this review highlights the applications of marker assisted selection (MAS), quantitative trait loci (QTL), genome wide association studies (GWAS) and the CRISPR/Cas-9 system for developing disease resistance against most important wheat diseases. We also reviewed all reported mapped QTLs for bunts, rusts, smuts, and nematode diseases of wheat. Furthermore, we have also proposed how the CRISPR/Cas-9 system and GWAS can assist breeders in the future for the genetic improvement of wheat. If these molecular approaches are used successfully in the future, they can be a significant step toward expanding food production in wheat crops.

Understanding the genomic selection for crop improvement: current progress and future prospects

Although increased use of modern breeding techniques and technology has resulted in long-term genetic gain, the pace of genetic gain must be sped up to satisfy global agricultural demand. However, marker-assisted selection has proven its potential for improving qualitative traits with large effects regulated by one to few genes. Its contribution to the improvement of the quantitative traits regulated by a number of small-effect genes is modest. In this context, genomic selection (GS) has been regarded as the most promising method for genetically enhancing complicated features that are regulated by several genes, each of which has minor effects. By examining a population's phenotypes and high-density marker scores, genomic selection can forecast the breeding potential of individual lines. The fact that GS uses all marker data in the prediction model prevents skewed marker effect estimations and maximizes the amount of variation caused by small-effect QTL. It has the ability to speed up the breeding cycle and as a consequence of which superior genotypes are selected rapidly. Developing the best GS models while taking into account non-additive effects, genotype-by-environment interaction, and cost-effectiveness will enable the widespread implementation of GS in plants. These steps will also increase heritability estimation and prediction accuracy. This review focuses on the shift from conventional selection methods to GS, underlying statistical tools and methodologies, the state of GS research in agricultural plants, and prospects for its effective use in the creation of climate-resilient crops.

Transcriptomic profiling of near-isogenic lines reveals candidate genes for a significant locus conferring metribuzin resistance in wheat

BACKGROUND

Weeds reduce wheat yields in dryland farming systems. Herbicides such as metribuzin are commonly used to control weeds. However, wheat has a narrow safety margin against metribuzin. Standing crops such as wheat with weeds in the same field can also be killed by the same dose of metribuzin. Therefore, it is important to identify metribuzin resistance genes and understand the resistance mechanism in wheat for sustainable crop production. A previous study identified a significant metribuzin resistance wheat QTL, Qsns.uwa.4 A.2, explaining 69% of the phenotypic variance for metribuzin resistance.

RESULTS

Two NIL pairs with the most contrasting performance in the metribuzin treatment and different in genetic backgrounds were compared using RNA sequence analysis, identifying nine candidate genes underlying Qsns.uwa.4 A.2 responsible for metribuzin resistance. Quantitative RT-qPCR further validated the candidate genes, with TraesCS4A03G1099000 (nitrate excretion transporter), TraesCS4A03G1181300 (aspartyl protease), and TraesCS4A03G0741300 (glycine-rich proteins) identified as key factors for metribuzin resistance.

CONCLUSION

Identified markers and key candidate genes can be used for selecting metribuzin resistance in wheat.

Molecular markers in tea plant (Camellia sinensis): Applications to evolution, genetic identification, and molecular breeding

Tea plants have a long cultivation history in the world, and the beverage (tea) made from its leaves is well known in the world. Due to the characteristics of self-incompatibility, long-term natural and artificial hybridization, tea plants have a very complex genetic background, which make the classification of tea plants unclear. Molecular marker, one type of genetic markers, has the advantages of stable inheritance, large amount of information, and high reliability. The development of molecular marker has facilitated the understanding of complex tea germplasm resources. So far, molecular markers had played important roles in the study of the origin and evolution, the preservation and identification of tea germplasms, and the excellent cultivars breeding of tea plants. However, the information is scattered, making it difficult to understand the advance of molecular markers in tea plants. In this paper, we summarized the development process and types of molecular markers in tea plants. In addition, the application advance of these molecular markers in tea plants was reviewed. Perspectives of molecular markers in tea plants were also systematically provided and discussed. The elaboration of molecular markers in this paper should help us to renew understanding of its application in tea plants.

From Transgenesis to Genome Editing in Crop Improvement: Applications, Marketing, and Legal Issues

The biotechnological approaches of transgenesis and the more recent eco-friendly new breeding techniques (NBTs), in particular, genome editing, offer useful strategies for genetic improvement of crops, and therefore, recently, they have been receiving increasingly more attention. The number of traits improved through transgenesis and genome editing technologies is growing, ranging from resistance to herbicides and insects to traits capable of coping with human population growth and climate change, such as nutritional quality or resistance to climatic stress and diseases. Research on both technologies has reached an advanced stage of development and, for many biotech crops, phenotypic evaluations in the open field are already underway. In addition, many approvals regarding main crops have been granted. Over time, there has been an increase in the areas cultivated with crops that have been improved through both approaches, but their use in various countries has been limited by legislative restrictions according to the different regulations applied which affect their cultivation, marketing, and use in human and animal nutrition. In the absence of specific legislation, there is an on-going public debate with favorable and unfavorable positions. This review offers an updated and in-depth discussion on these issues.

Breeding and Genomic Approaches towards Development of Fusarium Wilt Resistance in Chickpea

Chickpea is an important leguminous crop with potential to provide dietary proteins to both humans and animals. It also ameliorates soil nitrogen through biological nitrogen fixation. The crop is affected by an array of biotic and abiotic factors. Among different biotic stresses, a major fungal disease called Fusarium wilt, caused by Fusarium oxysporum f. sp. ciceris (FOC), is responsible for low productivity in chickpea. To date, eight pathogenic races of FOC (race 0, 1A, and 1B/C, 2-6) have been reported worldwide. The development of resistant cultivars using different conventional breeding methods is very time consuming and depends upon the environment. Modern technologies can improve conventional methods to solve these major constraints. Understanding the molecular response of chickpea to Fusarium wilt can help to provide effective management strategies. The identification of molecular markers closely linked to genes/QTLs has provided great potential for chickpea improvement programs. Moreover, omics approaches, including transcriptomics, metabolomics, and proteomics give scientists a vast viewpoint of functional genomics. In this review, we will discuss the integration of all available strategies and provide comprehensive knowledge about chickpea plant defense against Fusarium wilt.

Shade avoidance syndrome in soybean and ideotype toward shade tolerance

The shade avoidance syndrome (SAS) in soybean can have destructive effects on yield, as essential carbon resources reserved for yield are diverted to the petiole and stem for exaggerated elongation, resulting in lodging and susceptibility to disease. Despite numerous attempts to reduce the unfavorable impacts of SAS for the development of cultivars suitable for high-density planting or intercropping, the genetic bases and fundamental mechanisms of SAS remain largely unclear. The extensive research conducted in the model plant Arabidopsis provides a framework for understanding the SAS in soybean. Nevertheless, recent investigations suggest that the knowledge obtained from model Arabidopsis may not be applicable to all processes in soybean. Consequently, further efforts are required to identify the genetic regulators of SAS in soybean for molecular breeding of high-yield cultivars suitable for density farming. In this review, we present an overview of the recent developments in SAS studies in soybean and suggest an ideal planting architecture for shade-tolerant soybean intended for high-yield breeding.

Cruz PC, Borromeo TH, Lalusin AG, Mauleon R, McNally KL, Swamy BPM. Molecular dissection of connected rice populations revealed important genomic regions for agronomic and biofortification traits

Breeding staple crops with increased micronutrient concentration is a sustainable approach to address micronutrient malnutrition. We carried out Multi-Cross QTL analysis and Inclusive Composite Interval Mapping for 11 agronomic, yield and biofortification traits using four connected RILs populations of rice. Overall, MC-156 QTLs were detected for agronomic (115) and biofortification (41) traits, which were higher in number but smaller in effects compared to single population analysis. The MC-QTL analysis was able to detect important QTLs viz: qZn_5.2, qFe_7.1, qGY_10.1, qDF_7.1, qPH_1.1, qNT_4.1, qPT_4.1, qPL_1.2, qTGW_5.1, qGL_3.1 , and qGW_6.1 , which can be used in rice genomics assisted breeding. A major QTL (qZn_5.2 ) for grain Zn concentration has been detected on chromosome 5 that accounted for 13% of R². In all, 26 QTL clusters were identified on different chromosomes. qPH_6.1 epistatically interacted with qZn_5.1 and qGY_6.2 . Most of QTLs were co-located with functionally related candidate genes indicating the accuracy of QTL mapping. The genomic region of qZn_5.2 was co-located with putative genes such as OsZIP5, OsZIP9, and LOC_OS05G40490 that are involved in Zn uptake. These genes included polymorphic functional SNPs, and their promoter regions were enriched with cis-regulatory elements involved in plant growth and development, and biotic and abiotic stress tolerance. Major effect QTL identified for biofortification and agronomic traits can be utilized in breeding for Zn biofortified rice varieties.