Yearly Archives: 2023

Mapping QTL for vernalization requirement identified adaptive divergence of the candidate gene Flowering Locus C in polyploid Camelina sativa

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Abstract

Vernalization requirement is an integral component of flowering in winter-type plants. The availability of winter ecotypes among Camelina species facilitated the mapping of quantitative trait loci (QTL) for vernalization requirement in Camelina sativa. An inter and intraspecific crossing scheme between related Camelina species, where one spring and two different sources of winter-type habit were used, resulted in the development of two segregating populations. Linkage maps generated with sequence-based markers identified three QTLs associated with vernalization requirement in C. sativa; two from the interspecific (chromosomes 13 and 20) and one from the intraspecific cross (chromosome 8). Notably, the three loci were mapped to different homologous regions of the hexaploid C. sativa genome. All three QTLs were found in proximity to Flowering Locus C (FLC), variants of which have been reported to affect the vernalization requirement in plants. Temporal transcriptome analysis for winter-type Camelina alyssum demonstrated reduction in expression of FLC on chromosomes 13 and 20 during cold treatment, which would trigger flowering, since FLC would be expected to suppress floral initiation. FLC on chromosome 8 also showed reduced expression in the C. sativa ssp. pilosa winter parent upon cold treatment, but was expressed at very high levels across all time points in the spring-type C. sativa. The chromosome 8 copy carried a deletion in the spring-type line, which could impact its functionality. Contrary to previous reports, all three FLC loci can contribute to controlling the vernalization response in C. sativa and provide opportunities for manipulating this requirement in the crop.

A medium‐density genotyping platform for cultivated strawberry using DArTag technology

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Abstract

Genomic prediction in breeding populations containing hundreds to thousands of parents and seedlings is prohibitively expensive with current high-density genetic marker platforms designed for strawberry. We developed mid-density panels of molecular inversion probes (MIPs) to be deployed with the “DArTag” marker platform to provide a low-cost, high-throughput genotyping solution for strawberry genomic prediction. In total, 7742 target single nucleotide polymorphism (SNP) regions were used to generate MIP assays that were tested with a screening panel of 376 octoploid Fragaria accessions. We evaluated the performance of DArTag assays based on genotype segregation, amplicon coverage, and their ability to produce subgenome-specific amplicon alignments to the FaRR1 assembly and subsequent alignment-based variant calls with strong concordance to DArT's alignment-free, count-based genotype reports. We used a combination of marker performance metrics and physical distribution in the FaRR1 assembly to select 3K and 5K production panels for genotyping of large strawberry populations. We show that the 3K and 5K DArTag panels are able to target and amplify homologous alleles within subgenomic sequences with low-amplification bias between reference and alternate alleles, supporting accurate genotype calling while producing marker genotypes that can be treated as functionally diploid for quantitative genetic analysis. The 3K and 5K target SNPs show high levels of polymorphism in diverse F. × ananassa germplasm and UC Davis cultivars, with mean pairwise diversity (π) estimates of 0.40 and 0.32 and mean heterozygous genotype frequencies of 0.35 and 0.33, respectively.

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.