Soybean genetics, genomics, and breeding for improving nutritional value and reducing antinutritional traits in food and feed

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Abstract

Soybean [Glycine max (L.) Merr.] is a globally important crop due to its valuable seed composition, versatile feed, food, and industrial end-uses, and consistent genetic gain. Successful genetic gain in soybean has led to widespread adaptation and increased value for producers, processors, and consumers. Specific focus on the nutritional quality of soybean seed composition for food and feed has further elucidated genetic knowledge and bolstered breeding progress. Seed components are historical and current targets for soybean breeders seeking to improve nutritional quality of soybean. This article reviews genetic and genomic foundations for improvement of nutritionally important traits, such as protein and amino acids, oil and fatty acids, carbohydrates, and specific food-grade considerations; discusses the application of advanced breeding technology such as CRISPR/Cas9 in creating seed composition variations; and provides future directions and breeding recommendations regarding soybean seed composition traits.

Editorial Board

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Editorial Board

On the cover: Rice grains depicting health benefits such as low glycemic index, pigmented rice, and low chalk, as well as long slender grains which capture the major market share. Read the introduction to the special issue “Grain Quality and Nutritional Genomics for Breeding Next Generation Crops” lead by guest editors Drs. Manish Pandey, Reyazul Rouf Mir, and Nese Sreenivasulu: https://doi.org/10.1002/tpg2.20396. Photo credit: Nese Sreenivasulu, IRRI.


Impact of genotype‐calling methodologies on genome‐wide association and genomic prediction in polyploids

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Abstract

Discovery and analysis of genetic variants underlying agriculturally important traits are key to molecular breeding of crops. Reduced representation approaches have provided cost-efficient genotyping using next-generation sequencing. However, accurate genotype calling from next-generation sequencing data is challenging, particularly in polyploid species due to their genome complexity. Recently developed Bayesian statistical methods implemented in available software packages, polyRAD, EBG, and updog, incorporate error rates and population parameters to accurately estimate allelic dosage across any ploidy. We used empirical and simulated data to evaluate the three Bayesian algorithms and demonstrated their impact on the power of genome-wide association study (GWAS) analysis and the accuracy of genomic prediction. We further incorporated uncertainty in allelic dosage estimation by testing continuous genotype calls and comparing their performance to discrete genotypes in GWAS and genomic prediction. We tested the genotype-calling methods using data from two autotetraploid species, Miscanthus sacchariflorus and Vaccinium corymbosum, and performed GWAS and genomic prediction. In the empirical study, the tested Bayesian genotype-calling algorithms differed in their downstream effects on GWAS and genomic prediction, with some showing advantages over others. Through subsequent simulation studies, we observed that at low read depth, polyRAD was advantageous in its effect on GWAS power and limit of false positives. Additionally, we found that continuous genotypes increased the accuracy of genomic prediction, by reducing genotyping error, particularly at low sequencing depth. Our results indicate that by using the Bayesian algorithm implemented in polyRAD and continuous genotypes, we can accurately and cost-efficiently implement GWAS and genomic prediction in polyploid crops.

Exploring the competitive potential of Ralstonia pseudosolanacearum and Ralstonia solanacearum: Insights from a comparative adaptability study

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Exploring the competitive potential of Ralstonia pseudosolanacearum and Ralstonia solanacearum: Insights from a comparative adaptability study

Ralstonia pseudosolanacearum exhibits greater biochemical and pathogenic adaptability than R. solanacearum. Conversely, the latter demonstrates greater ecological and physiological adaptability.


Abstract

Bacterial wilt, caused by Ralstonia pseudosolanacearum (Rpsol) and R. solanacearum (Rsol), poses a significant challenge to solanaceous plant cultivation worldwide, particularly in tropical and subtropical regions. Even though Brazil is recognized as one of the centres of origin and diversity of Rsol, in certain regions of this large country there is an emerging prevalence of Rpsol in production fields. Therefore, this study aimed to comprehensively investigate the adaptive traits of Rpsol and Rsol using a polyphasic approach. A diverse collection of isolates from both species was assessed for their physiological, biochemical, ecological and pathogenic traits. Rsol isolates demonstrated greater adaptability to a broader range of temperature, salinity and pH. They also exhibited enhanced abilities in biofilm formation and bacteriocin production. Conversely, Rpsol isolates exhibited a broader utilization of carbon sources and displayed a wider spectrum of resistance to inhibitory substances. Moreover, they demonstrated higher infectivity towards different solanaceous hosts, showing a faster invasion and colonization process in the roots and stems of tomato plants compared to Rsol isolates. Based on our findings, we concluded that Rsol exhibited greater physiological and ecological adaptability, while Rpsol showed greater pathogenic and biochemical adaptability. These results suggest that the coexistence of both species is maintained through a balance of distinct traits within each species.

Genetic mapping of dynamic control of leaf angle across multiple canopy levels in maize

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Abstract

Optimizing leaf angle and other canopy architecture traits has helped modern maize (Zea mays L.) become adapted to higher planting densities over the last 60 years. Traditional investigations into genetic control of leaf angle have focused on one leaf or the average of multiple leaves; as a result, our understanding of genetic control across multiple canopy levels is still limited. To address this, genetic mapping across four canopy levels was conducted in the present study to investigate the genetic control of leaf angle across the canopy. We developed two populations of doubled haploid lines derived from three inbreds with distinct leaf angle phenotypes. These populations were genotyped with genotyping-by-sequencing and phenotyped for leaf angle at four different canopy levels over multiple years. To understand how leaf angle changes across the canopy, the four measurements were used to derive three additional traits. Composite interval mapping was conducted with the leaf-specific measurements and the derived traits. A set of 59 quantitative trait loci (QTLs) were uncovered for seven traits, and two genomic regions were consistently detected across multiple canopy levels. Additionally, seven genomic regions were found to contain consistent QTLs with either relatively stable or dynamic effects at different canopy levels. Prioritizing the selection of QTLs with dynamic effects across the canopy will aid breeders in selecting maize hybrids with the ideal canopy architecture that continues to maximize yield on a per area basis under increasing planting densities.

Differential aggressiveness of Austropuccinia psidii isolates from guava and rose apple upon cross‐inoculation

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Differential aggressiveness of Austropuccinia psidii isolates from guava and rose apple upon cross-inoculation

Austropuccinia psidii isolates from guava and rose apple showed high pathogenic specialization to their original hosts and were unable to sporulate in heterospecific host–pathogen combinations.


Abstract

Myrtle rust, caused by Austropuccinia psidii, has been associated with more than 480 plant species belonging to the family Myrtaceae. Intraspecific variability in pathogenicity has been reported among isolates of A. psidii from different hosts. However, there are few studies that have comparatively quantified the disease in guava (Psidium guajava) and rose apple (Syzygium jambos). The objective of this work was to quantify the pathogenic variability of A. psidii isolates collected from guava and rose apple in Brazil and to investigate the mechanisms of infection and colonization of the pathogen at the cellular level. The monocyclic components of the rust disease were evaluated on young leaves of rose apple and guava plants cross-inoculated with isolates from rose apple and guava. Pathogenic specialization of both A. psidii isolates for their respective hosts was confirmed in this work. The guava A. psidii isolate was able to infect and colonize rose apple leaf tissues but no sporulation occurred. Similarly, the rose apple A. psidii isolate infected guava plants but did not sporulate. Confocal laser scanning microscopy revealed that lobed haustoria were present within rose apple leaves at 2 days post-inoculation (dpi) with both isolates, which resulted in intense mesophyll colonization for both interactions at 9 dpi. The latter is remarkable because infection of rose apple with the guava A. psidii isolate did not result in mature rust pustules.

The genetic architecture of the adaptive potential of Arabidopsis thaliana in response to Pseudomonas syringae strains isolated from south‐west France

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The genetic architecture of the adaptive potential of Arabidopsis thaliana in response to Pseudomonas syringae strains isolated from south-west France

By conducting a GWAS on an ecologically relevant pathosystem, we identified a polygenic architecture underlying the adaptive potential of the response of Arabidopsis thaliana to a non-native Pseudomonas syringae pathogenic strain.


Abstract

Phytopathogens are a threat for global food production and security. Emergence or re-emergence of plant pathogens is highly dependent on the environmental conditions affecting pathogen spread and survival. Under climate change, a geographic expansion of pathogen distribution poleward has been observed, potentially resulting in disease outbreaks on crops and wild plants. Therefore, estimating the adaptive potential of plants to novel epidemics and describing the underlying genetic architecture is a primary need to propose agricultural management strategies reducing pathogen outbreaks and to breed novel plant cultivars adapted to pathogens that might spread under climate change. To address this challenge, we inoculated Pseudomonas syringae strains isolated from Arabidopsis thaliana populations from south-west of France on the highly genetically polymorphic TOU-A A. thaliana population from north-east France. While no adaptive potential was identified in response to most P. syringae strains, the TOU-A population displayed a variable disease response to the JACO-CL strain belonging to the P. syringae phylogroup 7 (PG7). This strain carried a reduced type III secretion system (T3SS) characteristic of the PG7 as well as flexible genomic traits and potential novel effectors. Genome-wide association mapping on 192 TOU-A accessions revealed a polygenic architecture of disease response to JACO-CL. The main quantitative trait locus (QTL) region encompasses two R genes and the AT5G18310 gene encoding ubiquitin hydrolase, a target of the AvrRpt2 P. syringae effector. Altogether, our results pave the way for a better understanding of the genetic and molecular basis of the adaptive potential in an ecologically relevant A. thaliana–P. syringae pathosystem.

Identification of a new Rsg1 allele conferring resistance to multiple greenbug biotypes from barley accessions PI 499276 and PI 566459

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Abstract

Greenbug [Schizaphis graminum (Rondani)] is a major insect pest that significantly affects barley production worldwide. The identification of novel greenbug resistance genes is crucial for sustainable barley production and global food security. To identify greenbug resistance genes from a US breeding line PI 499276 and a Chinese cultivar PI 566459, two F6:7 recombinant inbred line (RIL) populations developed from crosses Weskan × PI 499276 and Weskan × PI 566459 were phenotyped for responses to greenbug biotype E and genotyped using genotyping-by-sequencing (GBS). Linkage analysis using single nucleotide polymorphism and kompetitive allele-specific polymorphism (KASP) markers delimited the greenbug resistance genes from PI 499276 and PI 566459 to a 1.2 Mb genomic region between 666.5 and 667.7 Mb on the long arm of chromosome 3H in the Morex Hordeum vulgare r1 reference sequence. Allelism tests based on responses of four F2 populations to greenbug biotype E indicated that the greenbug resistance gene in PI 499276 and PI 566459 is either allelic or very close to Rsg1. Given that PI 499276 and PI 566459 shared the same unique resistance pattern to a set of 14 greenbug biotypes, which is different from those of other Rsg1 alleles, they carry a new Rsg1 allele. The greenbug resistance genes in Post 90, PI 499276/PI 566459, and WBDC 336 were designated as Rsg1.a1, Rsg1.a2, and Rsg1.a3, respectively. KASP markers KASP-Rsg1a3-1, KASP-Rsg1a3-2, and KASP160 can be used to tag Rsg1.a2 in barley breeding.

Identification of diagnostic KASP‐SNP markers for routine breeding activities in yam (Dioscorea spp.)

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Abstract

Maintaining genetic purity and true-to-type clone identification are important action steps in breeding programs. This study aimed to develop a universal set of kompetitive allele-specific polymerase chain reaction (KASP)-based single nucleotide polymorphism (SNP) markers for routine breeding activities. Ultra-low-density SNP markers were created using an initial set of 173,675 SNPs that were obtained from whole-genome resequencing of 333 diverse white Guinea yam (Dioscorea rotundata Poir) genotypes. From whole-genome resequencing data, 99 putative SNP markers were found and successfully converted to high-throughput KASP genotyping assays. The markers set was validated on 374 genotypes representing six yam species. Out of the 99 markers, 50 were highly polymorphic across the species and could distinguish different yam species and pedigree origins. The selected SNP markers classified the validation population based on the different yam species and identified potential duplicates within yam species. Through penalized analysis, the male parent of progenies involved in polycrosses was successfully predicted and validated. Our research was a trailblazer in validating KASP-based SNP assays for species identification, parental fingerprinting, and quality control (QC) and quality assurance (QA) in yam breeding programs.

A new wild emmer wheat panel allows to map new loci associated with resistance to stem rust at seedling stage

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Abstract

Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is a major wheat disease worldwide. A collection of 283 wild emmer wheat [Triticum turgidum L. subsp. dicoccoides (Körn. ex Asch. & Graebn.) Thell] accessions, representative of the entire Fertile Crescent region where wild emmer naturally occurs, was assembled, genotyped, and characterized for population structure, genetic diversity, and rate of linkage disequilibrium (LD) decay. Then, the collection was employed for mapping Pgt resistance genes, as a proof of concept of the effectiveness of genome-wide association studies in wild emmer. The collection was evaluated in controlled conditions for reaction to six common Pgt pathotypes (TPMKC, TTTTF, JRCQC, TRTTF, TTKSK/Ug99, and TKTTF). Most resistant accessions originated from the Southern Levant wild emmer lineage, with some showing a resistance reaction toward three to six tested races. Association analysis was conducted considering a 12K polymorphic single-nucleotide polymorphisms dataset, kinship relatedness between accessions, and population structure. Eleven significant marker–trait associations (MTA) were identified across the genome, which explained from 17% to up to 49% of phenotypic variance with an average 1.5 additive effect (based on the 1–9 scoring scale). The identified loci were either effective against single or multiple races. Some MTAs colocalized with known Pgt resistance genes, while others represent novel resistance loci useful for durum and bread wheat prebreeding. Candidate genes with an annotated function related to plant response to pathogens were identified at the regions linked to the resistance and defined according to the estimated small LD (about 126 kb), as typical of wild species.