Population genomic and genome-wide association studies of agroclimatic traits in sorghum

Are cereal grasses a single genetic system?

In 1993, a passionate and provocative call to arms urged cereal researchers to consider the taxon they study as a single genetic system and collaborate with each other. Since then, that group of scientists has seen their discipline blossom. In an attempt to understand what unity of genetic systems means and how the notion was borne out by later research, we survey the progress and prospects of cereal genomics: sequence assemblies, population-scale sequencing, resistance gene cloning and domestication genetics. Gene order may not be as extraordinarily well conserved in the grasses as once thought. Still, several recurring themes have emerged. The same ancestral molecular pathways defining plant architecture have been co-opted in the evolution of different cereal crops. Such genetic convergence as much as cross-fertilization of ideas between cereal geneticists has led to a rich harvest of genes that, it is hoped, will lead to improved varieties.

Genome organization and botanical diversity

The rich diversity of angiosperms, both the planet's dominant flora and the cornerstone of agriculture, is integrally intertwined with a distinctive evolutionary history. Here, we explore the interplay between angiosperm genome organization and botanical diversity, empowered by genomic approaches ranging from genetic linkage mapping to analysis of gene regulation. Commonality in the genetic hardware of plants has enabled robust comparative genomics that has provided a broad picture of angiosperm evolution and implicated both general processes and specific elements in contributing to botanical diversity. We argue that the hardware of plant genomes-both in content and in dynamics-has been shaped by selection for rather substantial differences in gene regulation between plants and animals such as maize and human, organisms of comparable genome size and gene number. Their distinctive genome content and dynamics may reflect in part the indeterminate development of plants that puts strikingly different demands on gene regulation than in animals. Repeated polyploidization of plant genomes and multiplication of individual genes together with extensive rearrangement and differential retention provide rich raw material for selection of morphological and/or physiological variations conferring fitness in specific niches, whether natural or artificial. These findings exemplify the burgeoning information available to employ in increasing knowledge of plant biology and in modifying selected plants to better meet human needs.

Globally deployed sorghum aphid resistance gene RMES1 is vulnerable to biotype shifts but is bolstered by RMES2

Durable host plant resistance (HPR) to insect pests is critical for sustainable agriculture. Natural variation exists for aphid HPR in sorghum (Sorghum bicolor), but the genetic architecture and phenotype have not been clarified and characterized for most sources. In order to assess the current threat of a sorghum aphid (Melanaphis sorghi) biotype shift, we characterized the phenotype of Resistance to Melanaphis sorghi 1 (RMES1) and additional HPR architecture in globally admixed populations selected under severe sorghum aphid infestation in Haiti. We found RMES1 reduces sorghum aphid fecundity but not bird cherry-oat aphid (Rhopalosiphum padi) fecundity, suggesting a discriminant HPR response typical of gene-for-gene interaction. A second resistant gene, Resistance to Melanaphis sorghi 2 (RMES2), was more frequent than RMES1 resistant alleles in landraces and historic breeding lines. RMES2 contributes early and mid-season aphid resistance in a segregating F2 population; however, RMES1 was only significant with mid-season fitness. In a fixed population with high sorghum aphid resistance, RMES1 and RMES2 were selected for demonstrating a lack of severe antagonistic pleiotropy. Associations with resistance colocated with cyanogenic glucoside biosynthesis genes support additional HPR sources. Globally, therefore, an HPR source vulnerable to biotype shift via selection pressure (RMES1) is bolstered by a second common source of resistance in breeding programs (RMES2), which may be staving off a biotype shift and is critical for sustainable sorghum production.

Major impacts of widespread structural variation on sorghum

Genetic diversity is critical to crop breeding and improvement, and dissection of the genomic variation underlying agronomic traits can both assist breeding and give insight into basic biological mechanisms. Although recent genome analyses in plants reveal many structural variants (SVs), most current studies of crop genetic variation are dominated by single-nucleotide polymorphisms (SNPs). The extent of the impact of SVs on global trait variation, as well as their utility in genome-wide selection, is not yet understood. In this study, we built an SV data set based on whole-genome resequencing of diverse sorghum lines (n = 363), validated the correlation of photoperiod sensitivity and variety type, and identified SV hotspots underlying the divergent evolution of cellulosic and sweet sorghum. In addition, we showed the complementary contribution of SVs for heritability of traits related to sorghum adaptation. Importantly, inclusion of SV polymorphisms in association studies revealed genotype-phenotype associations not observed with SNPs alone. Three-way genome-wide association studies (GWAS) based on whole-genome SNP, SV, and integrated SNP + SV data sets showed substantial associations between SVs and sorghum traits. The addition of SVs to GWAS substantially increased heritability estimates for some traits, indicating their important contribution to functional allelic variation at the genome level. Our discovery of the widespread impacts of SVs on heritable gene expression variation could render a plausible mechanism for their disproportionate impact on phenotypic variation. This study expands our knowledge of SVs and emphasizes the extensive impacts of SVs on sorghum.

Identification of genetic and environmental factors influencing aerial root traits that support biological nitrogen fixation in sorghum

Plant breeding and genetics play a major role in the adaptation of plants to meet human needs. The current requirement to make agriculture more sustainable can be partly met by a greater reliance on biological nitrogen fixation by symbiotic diazotrophic microorganisms that provide crop plants with ammonium. Select accessions of the cereal crop sorghum (Sorghum bicolor (L.) Moench) form mucilage-producing aerial roots that harbor nitrogen-fixing bacteria. Breeding programs aimed at developing sorghum varieties that support diazotrophs will benefit from a detailed understanding of the genetic and environmental factors contributing to aerial root formation. A genome-wide association study of the sorghum minicore, a collection of 242 landraces, and 30 accessions from the sorghum association panel was conducted in Florida and Wisconsin and under 2 fertilizer treatments to identify loci associated with the number of nodes with aerial roots and aerial root diameter. Sequence variation in genes encoding transcription factors that control phytohormone signaling and root system architecture showed significant associations with these traits. In addition, the location had a significant effect on the phenotypes. Concurrently, we developed F2 populations from crosses between bioenergy sorghums and a landrace that produced extensive aerial roots to evaluate the mode of inheritance of the loci identified by the genome-wide association study. Furthermore, the mucilage collected from aerial roots contained polysaccharides rich in galactose, arabinose, and fucose, whose composition displayed minimal variation among 10 genotypes and 2 fertilizer treatments. These combined results support the development of sorghums with the ability to acquire nitrogen via biological nitrogen fixation.

Extreme trait GWAS (Et-GWAS): Unraveling rare variants in the 3,000 rice genome

Identifying high-impact, rare genetic variants associated with specific traits is crucial for crop improvement. The 3,010 rice genome (3K RG) dataset offers a valuable resource for discovering genomic regions with potential applications in crop breeding. We used Extreme Trait GWAS (Et-GWAS), employing bulk pooling and allele frequency measurement to efficiently extract rare variants from the 3K RG. This innovative approach facilitates the detection of associations between genetic variants and target traits, concentrating and quantifying rare alleles. In our study, on grain yield under drought stress, Et-GWAS successfully identified five key genes (OsPP2C11, OsK5.2, OsIRO2, OsPEX1, and OsPWA1) known for enhancing yield under drought. In addition, we examined the overlap of our results with previously reported qDTY-QTLs and observed that OsUCH1 and OsUCH2 genes were located within qDTY2.2 We compared Et-GWAS with conventional GWAS, finding it effectively capturing most candidate genes associated with the target trait. Validation with resistant starch showed similar results. To enhance user-friendliness, we developed a GUI for Et-GWAS; https://et-gwas.shinyapps.io/Et-GWAS/.

Research on Genotype Markers for Plant Height and Assisted Breeding of Key Sorghum Resources in China

Dwarfing and the selection of optimal plant types constitute the primary focus of sorghum breeding. However, the lack of clarity regarding the gene types associated with plant height genes Dw1-Dw4 in the primary breeding materials has led to increased plant heights in improved offspring of the same plant height type, resulting in unsatisfactory morphological traits. This study aimed to elucidate the gene types related to plant height in breeding materials, validate the regulatory mechanisms, and establish a material improvement system. The goal was to achieve molecular-marker-assisted dwarf breeding through the detection of plant height genes and the test cross verification of main Chinese sorghum materials. Using 38 main male sterile lines and 57 main restorer lines of grain sorghum as materials, three plant height genes were detected and classified. Ninety-five F1 generation hybrids of these materials, along with typical materials, were measured at the wax maturity stage. Test cross results demonstrated that the variation in dw1-dw3 genes in the breeding materials significantly influenced the plant height of hybrid offspring. The main male sterile lines in Chinese sorghum predominantly exhibited the "three-dwarf" type of Kafir and its improved lines, characterized by the genotype (Dw1-Dw2-dw3-dw4). On the other hand, restorer lines mainly showcased the improved "two-dwarf" (Dw1-Dw2-dw3-dw4) genotype of the Kaoliang/Caudatum subspecies, along with the "three-dwarf" type of some Kafir and its improved lines. The test materials predominantly contained dw3 genes, with relatively fewer dw1 genes in the restorer lines. The primary restorer materials lacked the dw2 gene, and dw2 significantly influenced plant type. The increased plant height in improved offspring of the same plant height type material was attributed to differences in gene types. Therefore, the enhancement of plant height in breeding materials should prioritize the use of different methods in conjunction with Dw1 and Dw2 classification.

Pilot-scale genome-wide association mapping in diverse sorghum germplasms identified novel genetic loci linked to major agronomic, root and stomatal traits

This genome-wide association studies (GWAS) used a subset of 96 diverse sorghum accessions, constructed from a large collection of 219 accessions for mining novel genetic loci linked to major agronomic, root morphological and physiological traits. The subset yielded 43,452 high quality single nucleotide polymorphic (SNP) markers exhibiting high allelic diversity. Population stratification showed distinct separation between caudatum and durra races. Linkage disequilibrium (LD) decay was rapidly declining with increasing physical distance across all chromosomes. The initial 50% LD decay was ~ 5 Kb and background level was within ~ 80 Kb. This study detected 42 significant quantitative trait nucleotide (QTNs) for different traits evaluated using FarmCPU, SUPER and 3VmrMLM which were in proximity with candidate genes related and were co-localized in already reported quantitative trait loci (QTL) and phenotypic variance (R2) of these QTNs ranged from 3 to 20%. Haplotype validation of the candidate genes from this study resulted nine genes showing significant phenotypic difference between different haplotypes. Three novel candidate genes associated with agronomic traits were validated including Sobic.001G499000, a potassium channel tetramerization domain protein for plant height, Sobic.010G186600, a nucleoporin-related gene for dry biomass, and Sobic.002G022600 encoding AP2-like ethylene-responsive transcription factor for plant yield. Several other candidate genes were validated and associated with different root and physiological traits including Sobic.005G104100, peroxidase 13-related gene with root length, Sobic.010G043300, homologous to Traes_5BL_8D494D60C, encoding inhibitor of apoptosis with iWUE, and Sobic.010G125500, encoding zinc finger, C3HC4 type domain with Abaxial stomatal density. In this study, 3VmrMLM was more powerful than FarmCPU and SUPER for detecting QTNs and having more breeding value indicating its reliable output for validation. This study justified that the constructed subset of diverse sorghums can be used as a panel for mapping other key traits to accelerate molecular breeding in sorghum.

Multi-genome comprehensive identification of SSR/SV and development of molecular markers database to serve Sorghum bicolor (L.) breeding

BACKGROUND

As an important food and cash crop, identification of DNA molecular markers is of great significance for molecular marker-assisted breeding of Sorghum (Sorghum bicolor (L.) moench). Although some sorghum-related mutation databases have been published, the special SSR and SV databases still need to be constructed and updated.

RESULTS

In this study, the quality of 18 different sorghum genomes was evaluated, and two genomes were assembled at chromosome level. Through the identification and comparative analysis of SSR loci in these genomes, the distribution characteristics of SSR in the above sorghum genomes were initially revealed. At the same time, five representative reference genomes were selected to identify the structural variation of sorghum. Finally, a convenient SSR/SV database of sorghum was constructed by integrating the above results ( http://www.sorghum.top:8079/ ; http://43.154.129.150:8079/ ; http://47.106.184.91:8079/ ). Users can query the information of related sites and primer pairs.

CONCLUSIONS

Anyway, our research provides convenience for sorghum researchers and will play an active role in sorghum molecular marker-assisted breeding.

Regularized multi-trait multi-locus linear mixed models for genome-wide association studies and genomic selection in crops

BACKGROUND

We consider two key problems in genomics involving multiple traits: multi-trait genome wide association studies (GWAS), where the goal is to detect genetic variants associated with the traits; and multi-trait genomic selection (GS), where the emphasis is on accurately predicting trait values. Multi-trait linear mixed models build on the linear mixed model to jointly model multiple traits. Existing estimation methods, however, are limited to the joint analysis of a small number of genotypes; in fact, most approaches consider one SNP at a time. Estimating multi-dimensional genetic and environment effects also results in considerable computational burden. Efficient approaches that incorporate regularization into multi-trait linear models (no random effects) have been recently proposed to identify genomic loci associated with multiple traits (Yu et al. in Multitask learning using task clustering with applications to predictive modeling and GWAS of plant varieties. arXiv:1710.01788 , 2017; Yu et al in Front Big Data 2:27, 2019), but these ignore population structure and familial relatedness (Yu et al in Nat Genet 38:203-208, 2006).

RESULTS

This work addresses this gap by proposing a novel class of regularized multi-trait linear mixed models along with scalable approaches for estimation in the presence of high-dimensional genotypes and a large number of traits. We evaluate the effectiveness of the proposed methods using datasets in maize and sorghum diversity panels, and demonstrate benefits in both achieving high prediction accuracy in GS and in identifying relevant marker-trait associations.

CONCLUSIONS

The proposed regularized multivariate linear mixed models are relevant for both GWAS and GS. We hope that they will facilitate agronomy-related research in plant biology and crop breeding endeavors.

Discovering useful genetic variation in the seed parent gene pool for sorghum improvement

Multi-parent populations contain valuable genetic material for dissecting complex, quantitative traits and provide a unique opportunity to capture multi-allelic variation compared to the biparental populations. A multi-parent advanced generation inter-cross (MAGIC) B-line (MBL) population composed of 708 F6 recombinant inbred lines (RILs), was recently developed from four diverse founders. These selected founders strategically represented the four most prevalent botanical races (kafir, guinea, durra, and caudatum) to capture a significant source of genetic variation to study the quantitative traits in grain sorghum [Sorghum bicolor (L.) Moench]. MBL was phenotyped at two field locations for seven yield-influencing traits: panicle type (PT), days to anthesis (DTA), plant height (PH), grain yield (GY), 1000-grain weight (TGW), tiller number per meter (TN) and yield per panicle (YPP). High phenotypic variation was observed for all the quantitative traits, with broad-sense heritabilities ranging from 0.34 (TN) to 0.84 (PH). The entire population was genotyped using Diversity Arrays Technology (DArTseq), and 8,800 single nucleotide polymorphisms (SNPs) were generated. A set of polymorphic, quality-filtered markers (3,751 SNPs) and phenotypic data were used for genome-wide association studies (GWAS). We identified 52 marker-trait associations (MTAs) for the seven traits using BLUPs generated from replicated plots in two locations. We also identified desirable allelic combinations based on the plant height loci (Dw1, Dw2, and Dw3), which influences yield related traits. Additionally, two novel MTAs were identified each on Chr1 and Chr7 for yield traits independent of dwarfing genes. We further performed a multi-variate adaptive shrinkage analysis and 15 MTAs with pleiotropic effect were identified. The five best performing MBL progenies were selected carrying desirable allelic combinations. Since the MBL population was designed to capture significant diversity for maintainer line (B-line) accessions, these progenies can serve as valuable resources to develop superior sorghum hybrids after validation of their general combining abilities via crossing with elite pollinators. Further, newly identified desirable allelic combinations can be used to enrich the maintainer germplasm lines through marker-assisted backcross breeding.

Genetic dissection of root architecture in Ethiopian sorghum landraces

KEY MESSAGE

This study quantified genetic variation in root system architecture (root number, angle, length and dry mass) within a diversity panel of 1771 Ethiopian sorghum landraces and identified 22 genomic regions associated with the root variations. The root system architecture (RSA) of crop plants influences adaptation to water-limited conditions and determines the capacity of a plant to access soil water and nutrients. Four key root traits (number, angle, length and dry mass) were evaluated in a diversity panel of 1771 Ethiopian sorghum landraces using purpose-built root chambers. Significant genetic variation was observed in all studied root traits, with nodal root angle ranging from 16.4° to 26.6°, with a high repeatability of 78.9%. Genome wide association studies identified a total of 22 genomic regions associated with root traits which were distributed on all chromosomes except chromosome SBI-10. Among the 22 root genomic regions, 15 co-located with RSA trait QTL previously identified in sorghum, with the remaining seven representing novel RSA QTL. The majority (85.7%) of identified root angle QTL also co-localized with QTL previously identified for stay-green in sorghum. This suggests that the stay-green phenotype might be associated with root architecture that enhances water extraction during water stress conditions. The results open avenues for manipulating root phenotypes to improve productivity in abiotic stress environments via marker-assisted selection.

Genome-wide association study of resistance to anthracnose in pepper (Capsicum chinense) germplasm

BACKGROUND

Anthracnose is a fungal disease caused by Colletotrichum spp. that has a significant impact on worldwide pepper production. Colletotrichum scovillei is the most common pathogenic anthracnose-causing species in the Republic of Korea.

RESULTS

The resistances of 197 pepper (Capsicum chinense) accessions deposited in Korea's National Agrobiodiversity Center were evaluated for their response against the virulent pathogens Colletotrichum acutatum isolate 'KSCa-1' and C. scovillei isolate 'Hana') in the field and in vitro methods for three consecutive years (2018 to 2020). The severity of the disease was recorded and compared between inoculation methods. Six phenotypically resistant pepper accessions were selected based on three years of disease data. All of the selected resistant pepper accessions outperformed the control resistant pepper in terms of resistance (PI 594,137). A genome-wide association study (GWAS) was carried out to identify single nucleotide polymorphisms (SNPs) associated with anthracnose resistance. An association analysis was performed using 53,518 SNPs and the disease score of the 2020 field and in vitro experiment results. Both field and in vitro experiments revealed 25 and 32 significantly associated SNPs, respectively. These SNPs were found on all chromosomes except Ch06 and Ch07 in the field experiment, whereas in the in vitro experiment they were found on all chromosomes except Ch04 and Ch11.

CONCLUSION

In this study, six resistant C. chinense accessions were selected. Additionally, in this study, significantly associated SNPs were found in a gene that codes for a protein kinase receptor, such as serine/threonine-protein kinase, and other genes that are known to be involved in disease resistance. This may strengthen the role of these genes in the development of anthracnose resistance in Capsicum spp. As a result, the SNPs discovered to be strongly linked in this study can be used to identify a potential marker for selecting pepper material resistant to anthracnose, which will assist in the development of resistant varieties.

A first look at the ability to use genomic prediction for improving the ratooning ability of sugarcane

The sugarcane ratooning ability (RA) is the most important target trait for breeders seeking to enhance the profitability of sugarcane production by reducing the planting cost. Understanding the genetics governing the RA could help breeders by identifying molecular markers that could be used for genomics-assisted breeding (GAB). A replicated field trial was conducted for three crop cycles (plant cane, first ratoon, and second ratoon) using 432 sugarcane clones and used for conducting genome-wide association and genomic prediction of five sugar and yield component traits of the RA. The RA traits for economic index (EI), stalk population (SP), stalk weight (SW), tonns of cane per hectare (TCH), and tonns of sucrose per hectare (TSH) were estimated from the yield and sugar data. A total of six putative quantitative trait loci and eight nonredundant single-nucleotide polymorphism (SNP) markers were associated with all five tested RA traits and appear to be unique. Seven putative candidate genes were colocated with significant SNPs associated with the five RA traits. The genomic prediction accuracies for those tested traits were moderate and ranged from 0.21 to 0.36. However, the models fitting fixed effects for the most significant associated markers for each respective trait did not give any advantages over the standard models without fixed effects. As a result of this study, more robust markers could be used in the future for clone selection in sugarcane, potentially helping resolve the genetic control of the RA in sugarcane.

Plasticity of root hair and rhizosheath traits and their relationship to phosphorus uptake in sorghum

Sorghum is an essential crop for resilient and adaptive responses to climate change. The root systems of crop plants significantly contribute to the tolerance of abiotic stresses. There is little information on sorghum genotypes' root systems and plasticity to external P supply. In this paper, we investigated the variations in root systems, as well as the responses, trait relationships, and plasticity of two sorghum genotypes (Naga Red and Naga White), popularly grown in Ghana, to five external P concentrations ([P]ext): 0, 100, 200, 300, and 400 mg P kg-1 soil. Sorghum plants were grown in greenhouse pots and harvested for root trait measurements at the five-leaf and growing point differentiation (GPD) developmental stages. The plants were responsive to [P]ext and formed rhizosheaths. The two genotypes showed similar characteristics for most of the traits measured but differed significantly in total and lateral root lengths in favor of the red genotype. For example, at the five-leaf growth stage, the lateral root length of the red and white genotypes was 22.8 and 16.2 cm, respectively, but 124 and 88.9 cm, at the GPD stage. The responses and plasticity of the root system traits, including rhizosheath, to [P]ext were more prominent, positive, and linear at the five-leaf stage than at the GPD growth stage. At the five-leaf growth stage, total root length increased by about 2.5-fold with increasing [P]ext compared to the unamended soil. At the GPD stage, however, total root length decreased by about 1.83-fold as [P]ext increased compared to the unamended soil. Specific rhizosheath weight correlated with RHD, albeit weakly, and together explained up to 59% of the variation in tissue P. Root hair density was more responsive to P supply than root hair length and showed a similar total and lateral root length pattern. Most desirable responses to P occurred at a rate of 200-300 mg P kg-1 soil. It is concluded that sorghum would form rhizosheath, and [P]ext could be critical for the early vigorous growth of sorghum's responsive root and shoot traits. Beyond the early days of development, additional P application might be necessary to sustain the responses and plasticity observed during the early growth period, but this requires further investigation, potentially under field conditions.

Genetic Diversity and Population Structure of African Sorghum (Sorghum bicolor L. Moench) Accessions Assessed through Single Nucleotide Polymorphisms Markers

Assessing the genetic diversity and population structure of cultivated sorghum is important for heterotic grouping, breeding population development, marker-assisted cultivar development, and release. The objectives of the present study were to assess the genetic diversity and deduce the population structure of 200 sorghum accessions using diversity arrays technology (DArT)-derived single nucleotide polymorphism (SNP) markers. The expected heterozygosity values ranged from 0.10 to 0.50 with an average of 0.32, while the average observed heterozygosity (0.15) was relatively low, which is a typical value for autogamous crops species like sorghum. Moderate polymorphic information content (PIC) values were identified with a mean of 0.26, which indicates the informativeness of the chosen SNP markers. The population structure and cluster analyses revealed four main clusters with a high level of genetic diversity among the accessions studied. The variation within populations (41.5%) was significantly higher than that among populations (30.8%) and between samples within the structure (27.7%). The study identified distantly related sorghum accessions such as SAMSORG 48, KAURA RED GLUME; Gadam, AS 152; CSRO1, ICNSL2014-062; and YALAI, KAFI MORI. The accessions exhibited wide genetic diversity that will be useful in developing new gene pools and novel genotypes for West Africa sorghum breeding programs.

Association mapping reveals novel genes and genomic regions controlling grain size architecture in mini core accessions of Indian National Genebank wheat germplasm collection

Wheat (Triticum aestivum L.) is a staple food crop for the global human population, and thus wheat breeders are consistently working to enhance its yield worldwide. In this study, we utilized a sub-set of Indian wheat mini core germplasm to underpin the genetic architecture for seed shape-associated traits. The wheat mini core subset (125 accessions) was genotyped using 35K SNP array and evaluated for grain shape traits such as grain length (GL), grain width (GW), grain length, width ratio (GLWR), and thousand grain weight (TGW) across the seven different environments (E₁, E₂, E₃, E₄, E₅, E₅, E₆, and E₇). Marker-trait associations were determined using a multi-locus random-SNP-effect Mixed Linear Model (mrMLM) program. A total of 160 non-redundant quantitative trait nucleotides (QTNs) were identified for four grain shape traits using two or more GWAS models. Among these 160 QTNs, 27, 36, 38, and 35 QTNs were associated for GL, GW, GLWR, and TGW respectively while 24 QTNs were associated with more than one trait. Of these 160 QTNs, 73 were detected in two or more environments and were considered reliable QTLs for the respective traits. A total of 135 associated QTNs were annotated and located within the genes, including ABC transporter, Cytochrome450, Thioredoxin_M-type, and hypothetical proteins. Furthermore, the expression pattern of annotated QTNs demonstrated that only 122 were differentially expressed, suggesting these could potentially be related to seed development. The genomic regions/candidate genes for grain size traits identified in the present study represent valuable genomic resources that can potentially be utilized in the markers-assisted breeding programs to develop high-yielding varieties.

Genome-Wide Association Study of Seed Morphology Traits in Senegalese Sorghum Cultivars

Sorghum is considered the fifth most important crop in the world. Despite the potential value of Senegalese germplasm for various traits, such as resistance to fungal diseases, there is limited information on the study of sorghum seed morphology. In this study, 162 Senegalese germplasms were evaluated for seed area size, length, width, length-to-width ratio, perimeter, circularity, the distance between the intersection of length & width (IS) and center of gravity (CG), and seed darkness and brightness by scanning and analyzing morphology-related traits with SmartGrain software at the USDA-ARS Plant Science Research Unit. Correlations between seed morphology-related traits and traits associated with anthracnose and head smut resistance were analyzed. Lastly, genome-wide association studies were performed on phenotypic data collected from over 16,000 seeds and 193,727 publicly available single nucleotide polymorphisms (SNPs). Several significant SNPs were found and mapped to the reference sorghum genome to uncover multiple candidate genes potentially associated with seed morphology. The results indicate clear correlations among seed morphology-related traits and potential associations between seed morphology and the defense response of sorghum. GWAS analysis listed candidate genes associated with seed morphologies that can be used for sorghum breeding in the future.

Multi-Trait Genome-Wide Association Studies of Sorghum bicolor Regarding Resistance to Anthracnose, Downy Mildew, Grain Mold and Head Smut

Multivariate linear mixed models (mvLMMs) are widely applied for genome-wide association studies (GWAS) to detect genetic variants affecting multiple traits with correlations and/or different plant growth stages. Subsets of multiple sorghum populations, including the Sorghum Association Panel (SAP), the Sorghum Mini Core Collection and the Senegalese sorghum population, have been screened against various sorghum diseases such as anthracnose, downy mildew, grain mold and head smut. Still, these studies were generally performed in a univariate framework. In this study, we performed GWAS based on the principal components of defense-related multi-traits against the fungal diseases, identifying new potential SNPs (S04_51771351, S02_66200847, S09_47938177, S08_7370058, S03_72625166, S07_17951013, S04_66666642 and S08_51886715) associated with sorghum's defense against these diseases.

Recent advancements in the breeding of sorghum crop: current status and future strategies for marker-assisted breeding

Sorghum is emerging as a model crop for functional genetics and genomics of tropical grasses with abundant uses, including food, feed, and fuel, among others. It is currently the fifth most significant primary cereal crop. Crops are subjected to various biotic and abiotic stresses, which negatively impact on agricultural production. Developing high-yielding, disease-resistant, and climate-resilient cultivars can be achieved through marker-assisted breeding. Such selection has considerably reduced the time to market new crop varieties adapted to challenging conditions. In the recent years, extensive knowledge was gained about genetic markers. We are providing an overview of current advances in sorghum breeding initiatives, with a special focus on early breeders who may not be familiar with DNA markers. Advancements in molecular plant breeding, genetics, genomics selection, and genome editing have contributed to a thorough understanding of DNA markers, provided various proofs of the genetic variety accessible in crop plants, and have substantially enhanced plant breeding technologies. Marker-assisted selection has accelerated and precised the plant breeding process, empowering plant breeders all around the world.

Genome-wide association study reveals genomic loci influencing agronomic traits in Ethiopian sorghum (Sorghum bicolor (L.) Moench) landraces

Uncovering the genetic basis of agronomic traits in sorghum landraces that have adapted to various agro-climatic conditions would contribute to sorghum improvement efforts around the world. To identify quantitative trait nucleotides (QTNs) associated with nine agronomic traits in a panel of 304 sorghum accessions collected from diverse environments across Ethiopia (considered to be the center of origin and diversity), multi-locus genome-wide association studies (ML-GWAS) were performed using 79,754 high quality single nucleotide polymorphism (SNP) markers. Association analyses using six ML-GWAS models identified a set of 338 significantly (LOD ≥ 3)-associated QTNs for nine agronomic traits of sorghum accessions evaluated in two environments (E1 and E2) and their combined dataset (Em). Of these, 121 reliable QTNs, including 13 for flowering time (DF), 13 for plant height (PH), 9 for tiller number (TN), 15 for panicle weight (PWT), 30 for grain yield per panicle (GYP), 12 for structural panicle mass (SPM), 13 for hundred seed weight (HSW), 6 for grain number per panicle (GNP), and 10 for panicle exertion (PE) were consistently detected by at least three ML-GWAS methods and/or in two different environments. Notably, Ethylene responsive transcription factor gene AP2/ERF, known for regulation of plant growth, and the sorghum Terminal flower1/TF1 gene, which functions in the control of floral architecture, were identified as strong candidate genes associated with PH and HSW, respectively. This study provides an entry point for further validation studies to elucidate complex mechanisms controlling important agronomic traits in sorghum.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01381-5.

Functional genomic effects of indels using Bayesian genome-phenome wide association studies in sorghum

High-throughput genomic and phenomic data have enhanced the ability to detect genotype-to-phenotype associations that can resolve broad pleiotropic effects of mutations on plant phenotypes. As the scale of genotyping and phenotyping has advanced, rigorous methodologies have been developed to accommodate larger datasets and maintain statistical precision. However, determining the functional effects of associated genes/loci is expensive and limited due to the complexity associated with cloning and subsequent characterization. Here, we utilized phenomic imputation of a multi-year, multi-environment dataset using PHENIX which imputes missing data using kinship and correlated traits, and we screened insertions and deletions (InDels) from the recently whole-genome sequenced Sorghum Association Panel for putative loss-of-function effects. Candidate loci from genome-wide association results were screened for potential loss of function using a Bayesian Genome-Phenome Wide Association Study (BGPWAS) model across both functionally characterized and uncharacterized loci. Our approach is designed to facilitate in silico validation of associations beyond traditional candidate gene and literature-search approaches and to facilitate the identification of putative variants for functional analysis and reduce the incidence of false-positive candidates in current functional validation methods. Using this Bayesian GPWAS model, we identified associations for previously characterized genes with known loss-of-function alleles, specific genes falling within known quantitative trait loci, and genes without any previous genome-wide associations while additionally detecting putative pleiotropic effects. In particular, we were able to identify the major tannin haplotypes at the Tan1 locus and effects of InDels on the protein folding. Depending on the haplotype present, heterodimer formation with Tan2 was significantly affected. We also identified major effect InDels in Dw2 and Ma1, where proteins were truncated due to frameshift mutations that resulted in early stop codons. These truncated proteins also lost most of their functional domains, suggesting that these indels likely result in loss of function. Here, we show that the Bayesian GPWAS model is able to identify loss-of-function alleles that can have significant effects upon protein structure and folding as well as multimer formation. Our approach to characterize loss-of-function mutations and their functional repercussions will facilitate precision genomics and breeding by identifying key targets for gene editing and trait integration.

Characterization of grain carotenoids in global sorghum germplasm to guide genomics-assisted breeding strategies

BACKGROUND

Crop biofortification is a successful strategy to ameliorate Vitamin A deficiency. Sorghum is a good candidate for vitamin A biofortification, as it is a staple food in regions with high prevalence of vitamin A deficiency. β-carotene-the main provitamin A carotenoid-is below the target concentration in sorghum grain, therefore biofortification breeding is required. Previous studies found evidence that sorghum carotenoid variation is oligogenic, suggesting that marker-assisted selection can be an appropriate biofortification method. However, we hypothesize that sorghum carotenoids have both oligogenic and polygenic components of variation. Genomics-assisted breeding could accelerate breeding efforts, but there exists knowledge gaps in the genetics underlying carotenoid variation, as well as appropriate germplasm to serve as donors.

RESULTS

In this study, we characterized carotenoids in 446 accessions from the sorghum association panel and carotenoid panel using high-performance liquid chromatography, finding high carotenoid accessions not previously identified. Genome-wide association studies conducted with 345 accessions, confirmed that zeaxanthin epoxidase is a major gene underlying variation for not only zeaxanthin, but also lutein and β-carotene. High carotenoid lines were found to have limited genetic diversity, and originated predominantly from only one country. Potential novel genetic diversity for carotenoid content was identified through genomic predictions in 2,495 accessions of unexplored germplasm. Oligogenic variation of carotenoids was confirmed, as well as evidence for polygenic variation, suggesting both marker-assisted selection and genomic selection can facilitate breeding efforts.

CONCLUSIONS

Sorghum vitamin A biofortification could be beneficial for millions of people who rely on it as a dietary staple. Carotenoid content in sorghum is low, but high heritability suggests that increasing concentrations through breeding is possible. Low genetic diversity among high carotenoid lines might be the main limitation for breeding efforts, therefore further germplasm characterization is needed to assess the feasibility of biofortification breeding. Based on germplasm here evaluated, most countries' germplasm lacks high carotenoid alleles, thus pre-breeding will be needed. A SNP marker within the zeaxanthin epoxidase gene was identified as a good candidate for use in marker-assisted selection. Due to the oligogenic and polygenic variation of sorghum grain carotenoids, both marker-assisted selection and genomic selection can be employed to accelerate breeding efforts.

Insights into the genetic determination of tuber shape and eye depth in potato natural population based on autotetraploid potato genome

Potato is one of the world's most important food crops, with a time-consuming breeding process. In this study, we performed a genome-wide association (GWAS) analysis of the two important traits of potato tuber shape and eye depth, using the tetraploid potato genome (2n=4x=48) as a reference. A total of 370 potatoes were divided into three subgroups based on the principal component analysis and evolutionary tree analysis. The genetic diversity within subgroups is low (5.18×10^-5, 4.36×10^-5 and 4.24×10^-5). Genome-wide linkage disequilibrium (LD) analysis showed that their LD is about 60 Kb. GWAS analysis identified that 146 significant single nucleotide polymorphism (SNP) loci at Chr01A1:34.44-35.25 Mb and Chr02A1:28.35-28.54 Mb regions are significantly associated with potato tuber shape, and that three candidate genes that might be related to potato tuber traits, PLATZ transcription factor, UTP-glucose-1-phosphate uridylyltransferase and FAR1 DNA-binding domain, are in the association region of Chr02A1. GWAS analysis identified 53 significant SNP loci at Chr05A2: 49.644-50.146 Mb and Chr06A2: 25.866-26.384 Mb regions with robust associations with potato tuber eye depth. Hydrolase and methyltransferases are present in the association region of Chr05A2, and three CYPs are present in the association region of Chr06A2. Our findings suggested that these genes are closely associated with potato tuber shape and eye depth. Our study identified molecular markers and candidate genes for improving tetraploid potato tuber shape and eye depth and provided ideas and insights for tetraploid potato breeding.

A Gγ protein regulates alkaline sensitivity in crops

The use of alkaline salt lands for crop production is hindered by a scarcity of knowledge and breeding efforts for plant alkaline tolerance. Through genome association analysis of sorghum, a naturally high-alkaline-tolerant crop, we detected a major locus, Alkaline Tolerance 1 (AT1), specifically related to alkaline-salinity sensitivity. An at1 allele with a carboxyl-terminal truncation increased sensitivity, whereas knockout of AT1 increased tolerance to alkalinity in sorghum, millet, rice, and maize. AT1 encodes an atypical G protein γ subunit that affects the phosphorylation of aquaporins to modulate the distribution of hydrogen peroxide (H₂O₂)_. These processes appear to protect plants against oxidative stress by alkali. Designing knockouts of AT1 homologs or selecting its natural nonfunctional alleles could improve crop productivity in sodic lands.

Progress in rice sheath blight resistance research

Rice sheath blight (ShB) disease poses a major threat to rice yield throughout the world. However, the defense mechanisms against ShB in rice remain largely unknown. ShB resistance is a typical quantitative trait controlled by multiple genes. With the rapid development of molecular methods, many quantitative trait loci (QTLs) related to agronomic traits, biotic and abiotic stresses, and yield have been identified by genome-wide association studies. The interactions between plants and pathogens are controlled by various plant hormone signaling pathways, and the pathways synergistically or antagonistically interact with each other, regulating plant growth and development as well as the defense response. This review summarizes the regulatory effects of hormones including auxin, ethylene, salicylic acid, jasmonic acid, brassinosteroids, gibberellin, abscisic acid, strigolactone, and cytokinin on ShB and the crosstalk between the various hormones. Furthermore, the effects of sugar and nitrogen on rice ShB resistance, as well as information on genes related to ShB resistance in rice and their effects on ShB are also discussed. In summary, this review is a comprehensive description of the QTLs, hormones, nutrition, and other defense-related genes related to ShB in rice. The prospects of targeting the resistance mechanism as a strategy for controlling ShB in rice are also discussed.

Exploring the sorghum race level diversity utilizing 272 sorghum accessions genomic resources

Due to evolutionary divergence, sorghum race populations exhibit significant genetic and morphological variation. A k-mer-based sorghum race sequence comparison identified the conserved k-mers of all 272 accessions from sorghum and the race-specific genetic signatures identified the gene variability in 10,321 genes (PAVs). To understand sorghum race structure, diversity and domestication, a deep learning-based variant calling approach was employed in a set of genotypic data derived from a diverse panel of 272 sorghum accessions. The data resulted in 1.7 million high-quality genome-wide SNPs and identified selective signature (both positive and negative) regions through a genome-wide scan with different (iHS and XP-EHH) statistical methods. We discovered 2,370 genes associated with selection signatures including 179 selective sweep regions distributed over 10 chromosomes. Co-localization of these regions undergoing selective pressure with previously reported QTLs and genes revealed that the signatures of selection could be related to the domestication of important agronomic traits such as biomass and plant height. The developed k-mer signatures will be useful in the future to identify the sorghum race and for trait and SNP markers for assisting in plant breeding programs.

Responses of sorghum to cold stress: A review focused on molecular breeding

Climate change has led to the search for strategies to acclimatize plants to various abiotic stressors to ensure the production and quality of crops of commercial interest. Sorghum is the fifth most important cereal crop, providing several uses including human food, animal feed, bioenergy, or industrial applications. The crop has an excellent adaptation potential to different types of abiotic stresses, such as drought, high salinity, and high temperatures. However, it is susceptible to low temperatures compared with other monocotyledonous species. Here, we have reviewed and discussed some of the research results and advances that focused on the physiological, metabolic, and molecular mechanisms that determine sorghum cold tolerance to improve our understanding of the nature of such trait. Questions and opportunities for a comprehensive approach to clarify sorghum cold tolerance or susceptibility are also discussed.

Variation in mitogenome structural conformation in wild and cultivated lineages of sorghum corresponds with domestication history and plastome evolution

BACKGROUND

Mitochondria are organelles within eukaryotic cells that are central to the metabolic processes of cellular respiration and ATP production. However, the evolution of mitochondrial genomes (mitogenomes) in plants is virtually unknown compared to animal mitogenomes or plant plastids, due to complex structural variation and long stretches of repetitive DNA making accurate genome assembly more challenging. Comparing the structural and sequence differences of organellar genomes within and between sorghum species is an essential step in understanding evolutionary processes such as organellar sequence transfer to the nuclear genome as well as improving agronomic traits in sorghum related to cellular metabolism.

RESULTS

Here, we assembled seven sorghum mitochondrial and plastid genomes and resolved reticulated mitogenome structures with multilinked relationships that could be grouped into three structural conformations that differ in the content of repeats and genes by contig. The grouping of these mitogenome structural types reflects the two domestication events for sorghum in east and west Africa.

CONCLUSIONS

We report seven mitogenomes of sorghum from different cultivars and wild sources. The assembly method used here will be helpful in resolving complex genomic structures in other plant species. Our findings give new insights into the structure of sorghum mitogenomes that provides an important foundation for future research into the improvement of sorghum traits related to cellular respiration, cytonuclear incompatibly, and disease resistance.

Genome-Wide Detection of Quantitative Trait Loci and Prediction of Candidate Genes for Seed Sugar Composition in Early Mature Soybean

Seed sugar composition, mainly including fructose, glucose, sucrose, raffinose, and stachyose, is an important indicator of soybean [Glycine max (L.) Merr.] seed quality. However, research on soybean sugar composition is limited. To better understand the genetic architecture underlying the sugar composition in soybean seeds, we conducted a genome-wide association study (GWAS) using a population of 323 soybean germplasm accessions which were grown and evaluated under three different environments. A total of 31,245 single-nucleotide polymorphisms (SNPs) with minor allele frequencies (MAFs) ≥ 5% and missing data ≤ 10% were selected and used in the GWAS. The analysis identified 72 quantitative trait loci (QTLs) associated with individual sugars and 14 with total sugar. Ten candidate genes within the 100 Kb flanking regions of the lead SNPs across six chromosomes were significantly associated with sugar contents. According to GO and KEGG classification, eight genes were involved in the sugar metabolism in soybean and showed similar functions in Arabidopsis. The other two, located in known QTL regions associated with sugar composition, may play a role in sugar metabolism in soybean. This study advances our understanding of the genetic basis of soybean sugar composition and facilitates the identification of genes controlling this trait. The identified candidate genes will help improve seed sugar composition in soybean.

Host Determinants of Fungal Species Composition and Symptom Manifestation in the Sorghum Grain Mold Disease Complex

Sorghum grain mold (SGM) is an important multifungal disease complex affecting sorghum (Sorghum bicolor) production systems worldwide. SGM-affected sorghum grain can be contaminated with potent fumonisin mycotoxins produced by Fusarium verticillioides, a prevalent SGM-associated taxon. Historically, efforts to improve resistance to SGM have achieved only limited success. Classical approaches to evaluating SGM resistance are based solely on disease severity, which offers little insight regarding the distinct symptom manifestations within the disease complex. In this study, three novel phenotypes were developed to facilitate assessment of SGM symptom manifestation. A sorghum diversity panel composed of 390 accessions was inoculated with endogenous strains of F. verticillioides and evaluated for these phenotypes, as well as for the conventional panicle grain mold severity rating phenotype, in South Carolina, U.S.A., in 2017 and 2019. Distributions of phenotype values were examined, broad-sense heritability was estimated, and relationships to botanical race were explored. A typology of SGM symptom manifestations was developed to classify accessions using principal component analysis and k-means clustering, constituting a novel option for basing breeding decisions on SGM outcomes more nuanced than disease severity. Genome-wide association studies were performed using SGM trait data, resulting in the identification of 19 significant single nucleotide polymorphisms in linkage disequilibrium with a total of 86 gene models. Our findings provide a basis of exploratory evidence regarding the genetic architecture of SGM symptom manifestation and indicate that traits other than disease severity could be tractable targets for SGM resistance breeding.

Genome-wide association study of agronomical and root-related traits in spring barley collection grown under field conditions

The root system is a key component for plant survival and productivity. In particular, under stress conditions, developing plants with a better root architecture can ensure productivity. The objectives of this study were to investigate the phenotypic variation of selected root- and yield-related traits in a diverse panel of spring barley genotypes. By performing a genome-wide association study (GWAS), we identified several associations underlying the variations occurring in root- and yield-related traits in response to natural variations in soil moisture. Here, we report the results of the GWAS based on both individual single-nucleotide polymorphism markers and linkage disequilibrium (LD) blocks of markers for 11 phenotypic traits related to plant morphology, grain quality, and root system in a group of spring barley accessions grown under field conditions. We also evaluated the root structure of these accessions by using a nondestructive method based on electrical capacitance. The results showed the importance of two LD-based blocks on chromosomes 2H and 7H in the expression of root architecture and yield-related traits. Our results revealed the importance of the region on the short arm of chromosome 2H in the expression of root- and yield-related traits. This study emphasized the pleiotropic effect of this region with respect to heading time and other important agronomic traits, including root architecture. Furthermore, this investigation provides new insights into the roles played by root traits in the yield performance of barley plants grown under natural conditions with daily variations in soil moisture content.

Evaluating Introgression Sorghum Germplasm Selected at the Population Level While Exploring Genomic Resources as a Screening Method

To exploit the novel genetic diversity residing in tropical sorghum germplasm, an expansive backcross nested-association mapping (BC-NAM) resource was developed in which novel genetic diversity was introgressed into elite inbreds. A major limitation of exploiting this type of genetic resource in hybrid improvement programs is the required evaluation in hybrid combination of the vast number of BC-NAM populations and lines. To address this, the utility of genomic information was evaluated to predict the hybrid performance of BC-NAM populations. Two agronomically elite BC-NAM populations were chosen for evaluation in which elite inbred RTx436 was the recurrent parent. Each BC₁F₃ line was evaluated in hybrid combination with an elite tester in two locations with phenotypes of grain yield, plant height, and days to anthesis collected on all test cross hybrids. Lines from both populations were found to outperform their recurrent parent. Efforts to utilize genetic distance based on genotyping-by-sequence (GBS) as a predictive tool for hybrid performance was ineffective. However, utilizing genomic prediction models using additive and dominance GBLUP kernels to screen germplasm appeared to be an effective method to eliminate inferior-performing lines that will not be useful in a hybrid breeding program.

Genetic diversity and population structure of sorghum [Sorghum bicolor (L.) Moench] genotypes in Ethiopia as revealed by microsatellite markers

In the tropical and semi-arid regions of Africa, sorghum [Sorghum bicolor (L.) Moench] is mainly grown as a major food security crop. Understanding the extent and pattern of genetic variability is a prerequisite criterion for sorghum improvement and conservation. The genetic diversity and population structure of 100 genotypes of sorghum were profiled using 15 microsatellite loci. A total of 108 alleles, with an overall mean of 7.2 alleles per locus, were produced by all of the microsatellite loci used due to their high polymorphism. Polymorphic information content values ranging from 0.68 to 0.89 indicated that all of the loci are effective genetic tools for analysing the genetic structure of sorghum. Different diversity metrics were used to evaluate genetic diversity among populations, and Nei's gene diversity index ranged from 0.74 to 0.81 with an overall mean of 0.78. Poor genetic differentiation (FST: 0.02; p < 0.0001) was found, where 98% of entire variability was accounted by the within populations genetic variability, leaving only 2.32% among populations. The highest genetic differentiation and Nis's genetic distance were observed between the sorghum populations of the Southern Nation and Nationalities Peoples and Dire Dawa regions. Due to increased gene flow (Nm = 10.53), the clustering, principal coordinate analysis and STRUCTURE analysis failed to categorize the populations into genetically different groups corresponding to their geographic sampling areas. In general, it was found that the microsatellite loci were highly informative and therefore valuable genetic tools to unfold the genetic diversity and population structure of Ethiopian sorghum genotypes. Among the five populations studied, sorghum populations from Amhara and Oromia had the highest genetic variation, indicating that the regions could be perhaps hotspots for useful alleles for the development of better-performing genotypes, and also for designing appropriate germplasm management strategies.

Genome-Wide Association Studies of Seven Root Traits in Soybean (Glycine max L.) Landraces

Soybean [Glycine max (L.) Merr.], an important oilseed crop, is a low-cost source of protein and oil. In Southeast Asia and Africa, soybeans are widely cultivated for use as traditional food and feed and industrial purposes. Given the ongoing changes in global climate, developing crops that are resistant to climatic extremes and produce viable yields under predicted climatic conditions will be essential in the coming decades. To develop such crops, it will be necessary to gain a thorough understanding of the genetic basis of agronomic and plant root traits. As plant roots generally lie beneath the soil surface, detailed observations and phenotyping throughout plant development present several challenges, and thus the associated traits have tended to be ignored in genomics studies. In this study, we phenotyped 357 soybean landraces at the early vegetative (V2) growth stages and used a 180 K single-nucleotide polymorphism (SNP) soybean array in a genome-wide association study (GWAS) conducted to determine the phenotypic relationships among root traits, elucidate the genetic bases, and identify significant SNPs associated with root trait-controlling genomic regions/loci. A total of 112 significant SNP loci/regions were detected for seven root traits, and we identified 55 putative candidate genes considered to be the most promising. Our findings in this study indicate that a combined approach based on SNP array and GWAS analyses can be applied to unravel the genetic basis of complex root traits in soybean, and may provide an alternative high-resolution marker strategy to traditional bi-parental mapping. In addition, the identified SNPs, candidate genes, and diverse variations in the root traits of soybean landraces will serve as a valuable basis for further application in genetic studies and the breeding of climate-resilient soybeans characterized by improved root traits.

Breeding crops for drought-affected environments and improved climate resilience

Breeding climate-resilient crops with improved levels of abiotic and biotic stress resistance as a response to climate change presents both opportunities and challenges. Applying the framework of the "breeder's equation," which is used to predict the response to selection for a breeding program cycle, we review methodologies and strategies that have been used to successfully breed crops with improved levels of drought resistance, where the target population of environments (TPEs) is a spatially and temporally heterogeneous mixture of drought-affected and favorable (water-sufficient) environments. Long-term improvement of temperate maize for the US corn belt is used as a case study and compared with progress for other crops and geographies. Integration of trait information across scales, from genomes to ecosystems, is needed to accurately predict yield outcomes for genotypes within the current and future TPEs. This will require transdisciplinary teams to explore, identify, and exploit novel opportunities to accelerate breeding program outcomes; both improved germplasm resources and improved products (cultivars, hybrids, clones, and populations) that outperform and replace the products in use by farmers, in combination with modified agronomic management strategies suited to their local environments.

Exome-wide variation in a diverse barley panel reveals genetic associations with ten agronomic traits in Eastern landraces

Barley (Hordeum vulgare ssp. vulgare) was one of the first crops to be domesticated and is adapted to a wide range of environments. Worldwide barley germplasm collections possess valuable allelic variations that could further improve barley productivity. Although barley genomics has offered a global picture of allelic variation among varieties and its association with various agronomic traits, polymorphisms from East Asian varieties remain scarce. In this study, we analyzed exome polymorphisms in a panel of 274 barley varieties collected worldwide, including 137 varieties from East Asian countries and Ethiopia. We revealed the underlying population structure and conducted genome-wide association studies for ten agronomic traits. Moreover, we examined genome-wide associations for traits related to grain size such as awn length and glume length. Our results demonstrate the value of diverse barley germplasm panels containing Eastern varieties, highlighting their distinct genomic signatures relative to Western subpopulations.

Molecular Breeding and Drought Tolerance in Chickpea

Cicer arietinum L. is the third greatest widely planted imperative pulse crop worldwide, and it belongs to the Leguminosae family. Drought is the utmost common abiotic factor on plants, distressing their water status and limiting their growth and development. Chickpea genotypes have the natural ability to fight drought stress using certain strategies viz., escape, avoidance and tolerance. Assorted breeding methods, including hybridization, mutation, and marker-aided breeding, genome sequencing along with omics approaches, could be used to improve the chickpea germplasm lines(s) against drought stress. Root features, for instance depth and root biomass, have been recognized as the greatest beneficial morphological factors for managing terminal drought tolerance in the chickpea. Marker-aided selection, for example, is a genomics-assisted breeding (GAB) strategy that can considerably increase crop breeding accuracy and competence. These breeding technologies, notably marker-assisted breeding, omics, and plant physiology knowledge, underlined the importance of chickpea breeding and can be used in future crop improvement programmes to generate drought-tolerant cultivars(s).

Modulating physiological and transcriptional regulatory mechanisms for enhanced climate resilience in cereal crops

Climate change adversely affects the yield and productivity of cereal crops, which consequently impacts food security. Therefore, studying stress acclimation, particularly transcriptional patterns and morpho-physiological responses of cereal crops to different stresses, will provide insights into the molecular determinants underlying climate resilience. The availability of advanced tools and approaches has enabled the characterization of plants at morphological, physiological, biochemical, and molecular levels, which will lead to the identification of genomic regions regulating the stress responses at these levels. This will further facilitate using transgenic, breeding, or genome editing approaches to manipulate the identified regions (genes, alleles, or QTLs) to enhance stress resilience. Next-generation sequencing approaches have advanced the identification of causal genes and markers in the genomes through forward or reverse genetics. In this context, the review enumerates the progress of dissecting the molecular mechanisms underlying transcriptional and physiological responses of major cereals to climate-induced stresses. The review systematically discusses different tools and approaches available to study the response of plants to various stresses and identify the molecular determinants regulating stress-resilience. Further, the application of genomics-assisted breeding, transgene-, and targeted editing-based approaches for modulating the genetic determinants for enhanced climate resilience has been elaborated.

Conventional and Omics Approaches for Understanding the Abiotic Stress Response in Cereal Crops-An Updated Overview

Cereals have evolved various tolerance mechanisms to cope with abiotic stress. Understanding the abiotic stress response mechanism of cereal crops at the molecular level offers a path to high-yielding and stress-tolerant cultivars to sustain food and nutritional security. In this regard, enormous progress has been made in the omics field in the areas of genomics, transcriptomics, and proteomics. Omics approaches generate a massive amount of data, and adequate advancements in computational tools have been achieved for effective analysis. The combination of integrated omics and bioinformatics approaches has been recognized as vital to generating insights into genome-wide stress-regulation mechanisms. In this review, we have described the self-driven drought, heat, and salt stress-responsive mechanisms that are highlighted by the integration of stress-manipulating components, including transcription factors, co-expressed genes, proteins, etc. This review also provides a comprehensive catalog of available online omics resources for cereal crops and their effective utilization. Thus, the details provided in the review will enable us to choose the appropriate tools and techniques to reduce the negative impacts and limit the failures in the intensive crop improvement study.

Genome-wide analyses using multi-locus models revealed marker-trait associations for major agronomic traits in Sorghum bicolor

Globally, sorghum is the fifth most important cereal crop, and it is a major crop in Ethiopia, where it has a high genetic diversity. The country's sorghum gene pool contributes significantly to sorghum improvement worldwide. This study aimed to identify genomic regions and candidate genes associated with major agronomic traits in sorghum by using its genetic resources in Ethiopia for a genome-wide association study (GWAS). Phenotypic data of days to flowering (DTF), plant height (PH), panicle length (PALH), panicle width (PAWD), panicle weight (PAWT), and grain yield (GY) were collected from a GWAS panel comprising 324 sorghum accessions grown in three environments. SeqSNP, a targeted genotyping method, was used to genotype the panel using 5,000 gene-based single nucleotide polymorphism (SNP) markers. For marker-trait association (MTA) analyses, fixed and random model circulating probability unification (FarmCPU), and Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK) models were used. In all traits, high phenotypic variation was observed, with broad-sense heritability ranging from 0.32 (for GY) to 0.90 (for PALH). A population structure, principal component analysis, and kinship analysis revealed that the accessions could be divided into two groups. In total, 54 MTAs were identified, 11 of which were detected by both BLINK and farmCPU. MTAs identified for each trait ranged from five (PAWT and GY) to fourteen (PH) representing both novel and previously identified quantitative trait loci (QTLs). Three SNPs were associated with more than one trait, including a SNP within the Sobic.004G189200 gene that was associated with PH and PAWT. Major effect SNP loci, Sbi2393610 (PVE = 23.3%), Sbi10438246 (PVE = 35.2%), Sbi17789352 (PVE = 11.9%) and Sbi30169733 (PVE = 18.9%) on chromosomes 1, 3, 5 and 9 that showed strong association signals for PAWD, DTF, GY and PALH, respectively, were major findings of this study. The SNP markers and candidate genes identified in this study provide insights into the genetic control of grain yield and related agronomic traits, and once validated, the markers could be used in genomics-led breeding.

Regulation of cyanogenic glucosides in wild and domesticated Eusorghum taxa

Domesticated sorghum (Sorghum bicolor [L.] Moench subsp. bicolor) diverts significant amounts of nitrogen away from primary metabolism to the synthesis of cyanogenic glucosides (CNglc) - specialized metabolites that release toxic hydrogen cyanide (HCN). Our aim was to identify the point in the genus Sorghum Moench at which plants gained the ability to maintain hazardous concentrations of cyanogenic glucosides in their leaves into maturity (HCN potential >0.4 mg g^-1 ). This ability occurs in domesticated sorghum (in the subgenus Eusorghum), but not in wild taxa in other Sorghum subgenera. Eight accessions from the subgenus Eusorghum were grown in a common garden: an improved sorghum line, five sorghum landraces, the crop's wild progenitor (S. bicolor subsp. verticilliflorum [Steud.] de Wet ex Wiersema & J. Dahlb.) and wild Sorghum propinquum (Kunth) Hitchc. HCN potential was measured in plants (n = 80) at the three-leaf stage and at 6 weeks old. All study accessions, including the wild taxa, had hazardous CNglc concentrations in the leaves at both the three-leaf stage (mean HCN potentials > = 2.5 mg g^-1 ) and at 6 weeks old (mean HCN potentials > = 0.68 mg g^-1 ), greatly contrasting the much lower mature leaf HCN potentials previously found in wild Sorghum taxa outside subgenus Eusorghum (generally <= 0.01 mg g^-1 ). Our results suggest that the ability to maintain hazardous leaf HCN potentials into maturity might have arisen during the divergence of Eusorghum from other Sorghum subgenera, rather than during the speciation or domestication of S. bicolor, and highlights the value of utilizing Sorghum taxa outside Eusorghum in efforts to improve the crop safety of sorghum.

Genetic analysis of seed traits in Sorghum bicolor that affect the human gut microbiome

Prebiotic fibers, polyphenols and other molecular components of food crops significantly affect the composition and function of the human gut microbiome and human health. The abundance of these, frequently uncharacterized, microbiome-active components vary within individual crop species. Here, we employ high throughput in vitro fermentations of pre-digested grain using a human microbiome to identify segregating genetic loci in a food crop, sorghum, that alter the composition and function of human gut microbes. Evaluating grain produced by 294 sorghum recombinant inbreds identifies 10 loci in the sorghum genome associated with variation in the abundance of microbial taxa and/or microbial metabolites. Two loci co-localize with sorghum genes regulating the biosynthesis of condensed tannins. We validate that condensed tannins stimulate the growth of microbes associated with these two loci. Our work illustrates the potential for genetic analysis to systematically discover and characterize molecular components of food crops that influence the human gut microbiome.

Diet affects the human gut microbiome, but studies linking crop genetics to seed traits that influence the human gut microbiome are lacking. Here, the authors develop an in vitro microbiome screening method and reveal the association between sorghum genes regulating condensed tannin biosynthesis and human gut microbiome.

Natural variation further increases resilience of sorghum bred for chronically drought-prone environments

Drought stress is one of the major constraints for crop production in the Sahel region of Africa. Here, we explore the potential to use natural genetic variation to build on the inherent drought tolerance of an elite sorghum cultivar, Teshale, that has been bred for Ethiopian conditions including chronic drought. We evaluated a backcross nested-association mapping population using 12 diverse founder lines crossed with Teshale under three drought-prone environments in Ethiopia. All 12 populations averaged higher head exsertion and lower leaf senescence than the recurrent parent in the two most stressful environments, reflecting new drought resilience mechanisms from the donors. A total of 154 quantitative trait loci (QTLs) were detected for eight drought-responsive traits, and their validity was supported by the fact that 113 (73.4%) overlapped with QTLs previously detected for the same traits, concentrated in regions previously associated with 'stay-green' traits. Allele effects showed that some favourable alleles are already present in the Ethiopian cultivar; however, the exotic donors offer rich scope for increasing drought resilience. Using model-selected SNPs associated with the eight traits identified in this study and three in a companion study, phenotypic prediction accuracies for grain yield were equivalent to genome-wide SNPs and were significantly better than random SNPs, indicating that the selected traits are predictive of sorghum grain yield.

Genetic basis of sorghum leaf width and its potential as a surrogate for transpiration efficiency

Leaf width was correlated with plant-level transpiration efficiency and associated with 19 QTL in sorghum, suggesting it could be a surrogate for transpiration efficiency in large breeding program. Enhancing plant transpiration efficiency (TE) by reducing transpiration without compromising photosynthesis and yield is a desirable selection target in crop improvement programs. While narrow individual leaf width has been correlated with greater intrinsic water use efficiency in C₄ species, the extent to which this translates to greater plant TE has not been investigated. The aims of this study were to evaluate the correlation of leaf width with TE at the whole-plant scale and investigate the genetic control of leaf width in sorghum. Two lysimetry experiments using 16 genotypes varying for stomatal conductance and three field trials using a large sorghum diversity panel (n = 701 lines) were conducted. Negative associations of leaf width with plant TE were found in the lysimetry experiments, suggesting narrow leaves may result in reduced plant transpiration without trade-offs in biomass accumulation. A wide range in width of the largest leaf was found in the sorghum diversity panel with consistent ranking among sorghum races, suggesting that environmental adaptation may have a role in modifying leaf width. Nineteen QTL were identified by genome-wide association studies on leaf width adjusted for flowering time. The QTL identified showed high levels of correspondence with those in maize and rice, suggesting similarities in the genetic control of leaf width across cereals. Three a priori candidate genes for leaf width, previously found to regulate dorsoventrality, were identified based on a 1-cM threshold. This study provides useful physiological and genetic insights for potential manipulation of leaf width to improve plant adaptation to diverse environments.

Lipidomics-Assisted GWAS (lGWAS) Approach for Improving High-Temperature Stress Tolerance of Crops

High-temperature stress (HT) over crop productivity is an important environmental factor demanding more attention as recent global warming trends are alarming and pose a potential threat to crop production. According to the Sixth IPCC report, future years will have longer warm seasons and frequent heat waves. Thus, the need arises to develop HT-tolerant genotypes that can be used to breed high-yielding crops. Several physiological, biochemical, and molecular alterations are orchestrated in providing HT tolerance to a genotype. One mechanism to counter HT is overcoming high-temperature-induced membrane superfluidity and structural disorganizations. Several HT lipidomic studies on different genotypes have indicated the potential involvement of membrane lipid remodelling in providing HT tolerance. Advances in high-throughput analytical techniques such as tandem mass spectrometry have paved the way for large-scale identification and quantification of the enormously diverse lipid molecules in a single run. Physiological trait-based breeding has been employed so far to identify and select HT tolerant genotypes but has several disadvantages, such as the genotype-phenotype gap affecting the efficiency of identifying the underlying genetic association. Tolerant genotypes maintain a high photosynthetic rate, stable membranes, and membrane-associated mechanisms. In this context, studying the HT-induced membrane lipid remodelling, resultant of several up-/down-regulations of genes and post-translational modifications, will aid in identifying potential lipid biomarkers for HT tolerance/susceptibility. The identified lipid biomarkers (LIPIDOTYPE) can thus be considered an intermediate phenotype, bridging the gap between genotype–phenotype (genotype–LIPIDOTYPE–phenotype). Recent works integrating metabolomics with quantitative genetic studies such as GWAS (mGWAS) have provided close associations between genotype, metabolites, and stress-tolerant phenotypes. This review has been sculpted to provide a potential workflow that combines MS-based lipidomics and the robust GWAS (lipidomics assisted GWAS-lGWAS) to identify membrane lipid remodelling related genes and associations which can be used to develop HS tolerant genotypes with enhanced membrane thermostability (MTS) and heat stable photosynthesis (HP).

Sorghum Association Panel whole-genome sequencing establishes cornerstone resource for dissecting genomic diversity

Association mapping panels represent foundational resources for understanding the genetic basis of phenotypic diversity and serve to advance plant breeding by exploring genetic variation across diverse accessions. We report the whole-genome sequencing (WGS) of 400 sorghum (Sorghum bicolor (L.) Moench) accessions from the Sorghum Association Panel (SAP) at an average coverage of 38× (25-72×), enabling the development of a high-density genomic marker set of 43 983 694 variants including single-nucleotide polymorphisms (approximately 38 million), insertions/deletions (indels) (approximately 5 million), and copy number variants (CNVs) (approximately 170 000). We observe slightly more deletions among indels and a much higher prevalence of deletions among CNVs compared to insertions. This new marker set enabled the identification of several novel putative genomic associations for plant height and tannin content, which were not identified when using previous lower-density marker sets. WGS identified and scored variants in 5-kb bins where available genotyping-by-sequencing (GBS) data captured no variants, with half of all bins in the genome falling into this category. The predictive ability of genomic best unbiased linear predictor (GBLUP) models was increased by an average of 30% by using WGS markers rather than GBS markers. We identified 18 selection peaks across subpopulations that formed due to evolutionary divergence during domestication, and we found six F_st peaks resulting from comparisons between converted lines and breeding lines within the SAP that were distinct from the peaks associated with historic selection. This population has served and continues to serve as a significant public resource for sorghum research and demonstrates the value of improving upon existing genomic resources.

Genetic and genomic diversity in the sorghum gene bank collection of Uganda

BACKGROUND

The Plant Genetic Resources Centre at the Uganda National Gene Bank houses has over 3000 genetically diverse landraces and wild relatives of Sorghum bicolor accessions. This genetic diversity resource is untapped, under-utilized, and has not been systematically incorporated into sorghum breeding programs. In this study, we characterized the germplasm collection using whole-genome SNP markers (DArTseq). Discriminant analysis of principal components (DAPC) was implemented to study the racial ancestry of the accessions in comparison to a global sorghum diversity set and characterize the sub-groups present in the Ugandan (UG) germplasm.

RESULTS

Population structure and phylogenetic analysis revealed the presence of five subgroups among the Ugandan accessions. The samples from the highlands of the southwestern region were genetically distinct as compared to the rest of the population. This subset was predominated by the caudatum race and unique in comparison to the other sub-populations. In this study, we detected QTL for juvenile cold tolerance by genome-wide association studies (GWAS) resulting in the identification of 4 markers associated (-log10p > 3) to survival under cold stress under both field and climate chamber conditions, located on 3 chromosomes (02, 06, 09). To our best knowledge, the QTL on Sb09 with the strongest association was discovered for the first time.

CONCLUSION

This study demonstrates how genebank genomics can potentially facilitate effective and efficient usage of valuable, untapped germplasm collections for agronomic trait evaluation and subsequent allele mining. In face of adverse climate change, identification of genomic regions potentially involved in the adaptation of Ugandan sorghum accessions to cooler climatic conditions would be of interest for the expansion of sorghum production into temperate latitudes.

Genome-wide identification and analysis of ACP gene family in Sorghum bicolor (L.) Moench

BACKGROUND

Acyl carrier proteins (ACP) constitute a very conserved carrier protein family. Previous studies have found that ACP not only takes part in the fatty acid synthesis process of almost all organisms, but also participates in the regulation of plant growth, development, and metabolism, and makes plants adaptable to stresses. However, this gene family has not been systematically studied in sorghum.

RESULTS

Nine ACP family members were identified in the sorghum genome, which were located on chromosomes 1, 2, 5, 7, 8 and 9, respectively. Evolutionary analysis among different species divided the ACP family into four subfamilies, showing that the SbACPs were more closely related to maize. The prediction results of subcellular localization showed that SbACPs were mainly distributed in chloroplasts and mitochondria, while fluorescence localization showed that SbACPs were mainly localized in chloroplasts in tobacco leaf. The analysis of gene structure revealed a relatively simple genetic structure, that there were 1-3 introns in the sorghum ACP family, and the gene structure within the same subfamily had high similarity. The amplification method of SbACPs was mainly large fragment replication, and SbACPs were more closely related to ACPs in maize and rice. In addition, three-dimensional structure analysis showed that all ACP genes in sorghum contained four α helices, and the second helix structure was more conserved, implying a key role in function. Cis-acting element analysis indicated that the SbACPs might be involved in light response, plant growth and development regulation, biotic and abiotic stress response, plant hormone regulation, and other physiological processes. What's more, qRT-PCR analysis uncovered that some of SbACPs might be involved in the adaptive regulation of drought and salt stresses, indicating the close relationship between fatty acids and the resistance to abiotic stresses in sorghum.

CONCLUSIONS

In summary, these results showed a comprehensive overview of the SbACPs and provided a theoretical basis for further studies on the biological functions of SbACPs in sorghum growth, development and abiotic stress responses.