A set of additive loci for seed oil content were identified using association mapping and one of the novel loci on the chromosome A5 was validated by linkage mapping.
 
Increasing seed oil content is one of the most important goals in the breeding of oilseed crops including Brassica napus, yet the genetic basis for variations in this important trait remains unclear. By genome-wide association study of seed oil content using 521 B. napus accessions genotyped with the Brassica 60K SNP array, we identified 50 loci significantly associated with seed oil content using three statistical models, the general linear model, the mixed linear model and the Anderson–Darling test. Together, the identified loci could explain approximately 80 % of the total phenotypic variance, and 29 of these loci have not been reported previously. Furthermore, a novel locus on the chromosome A5 that could increase 1.5–1.7 % of seed oil content was validated in an independent bi-parental linkage population. Haplotype analysis showed that the favorable alleles for seed oil content exhibit cumulative effects. Our results thus provide valuable information for understanding the genetic control of seed oil content in B. napus and may facilitate marker-based breeding for a higher seed oil content in this important oil crop.

A genome-wide association study reveals novel elite allelic variations in seed oil content of Brassica napus.

Current trends in population growth and consumption patterns continue to increase the demand for wheat, a key cereal for global food security. Further, multiple abiotic challenges due to climate change and evolving pathogen and pests continue to pose a major concern for increasing wheat production globally. Triticeae species comprising of primary, secondary and tertiary gene pools represent a rich source of genetic diversity in wheat. The conventional breeding strategies of direct hybridization, backcrossing and selection have successfully introgressed a number of desirable traits associated with grain yield, adaptation to abiotic stresses, disease resistance, and bio-fortification of wheat varieties. However, it is time consuming to incorporate genes conferring tolerance/resistance to multiple stresses in a single wheat variety by conventional approaches due to limitations in screening methods and the lower probabilities of combining desirable alleles. Efforts on developing innovative breeding strategies, novel tools and utilizing genetic diversity for new genes/alleles are essential to improve productivity, reduce vulnerability to diseases and pests and enhance nutritional quality. New technologies of high-throughput phenotyping, genome sequencing and genomic selection are promising approaches to maximize progeny screening and selection to accelerate the genetic gains in breeding more productive varieties. Use of cisgenic techniques to transfer beneficial alleles and their combinations within related species also offer great promise especially to achieve durable rust resistance.

/pdf/harnessing-diversity-in-wheat-to-enhance-grain-yield-climate-1pc16j7qrh.pdf

Harnessing Diversity in Wheat to Enhance Grain Yield, Climate Resilience, Disease and Insect Pest Resistance and Nutrition Through Conventional and Modern Breeding Approaches.

Summary
Gossypium hirsutum L. represents the largest source of textile fibre, and China is one of the largest cotton-producing and cotton-consuming countries in the world. To investigate the genetic architecture of the agronomic traits of upland cotton in China, a diverse and nationwide population containing 503 G. hirsutum accessions was collected for a genome-wide association study (GWAS) on 16 agronomic traits. The accessions were planted in four places from 2012 to 2013 for phenotyping. The CottonSNP63K array and a published high-density map based on this array were used for genotyping. The 503 G. hirsutum accessions were divided into three subpopulations based on 11 975 quantified polymorphic single-nucleotide polymorphisms (SNPs). By comparing the genetic structure and phenotypic variation among three genetic subpopulations, seven geographic distributions and four breeding periods, we found that geographic distribution and breeding period were not the determinants of genetic structure. In addition, no obvious phenotypic differentiations were found among the three subpopulations, even though they had different genetic backgrounds. A total of 324 SNPs and 160 candidate quantitative trait loci (QTL) regions were identified as significantly associated with the 16 agronomic traits. A network was established for multieffects in QTLs and interassociations among traits. Thirty-eight associated regions had pleiotropic effects controlling more than one trait. One candidate gene, Gh_D08G2376, was speculated to control the lint percentage (LP). This GWAS is the first report using high-resolution SNPs in upland cotton in China to comprehensively investigate agronomic traits, and it provides a fundamental resource for cotton genetic research and breeding.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/pbi.12722

Population structure and genetic basis of the agronomic traits of upland cotton in China revealed by a genome-wide association study using high-density SNPs

Cadmium (Cd) is a major environmental contaminant due to its widespread industrial use. Cd contamination of soil and water is rather classical but has emerged as a recent problem. Cd toxicity causes a range of damages to plants ranging from germination to yield suppression. Plant physiological functions, i.e., water interactions, essential mineral uptake, and photosynthesis, are also harmed by Cd. Plants have also shown metabolic changes because of Cd exposure either as direct impact on enzymes or other metabolites, or because of its propensity to produce reactive oxygen species, which can induce oxidative stress. In recent years, there has been increased interest in the potential of plants with ability to accumulate or stabilize Cd compounds for bioremediation of Cd pollution. Here, we critically review the chemistry of Cd and its dynamics in soil and the rhizosphere, toxic effects on plant growth, and yield formation. To conserve the environment and resources, chemical/biological remediation processes for Cd and their efficacy have been summarized in this review. Modulation of plant growth regulators such as cytokinins, ethylene, gibberellins, auxins, abscisic acid, polyamines, jasmonic acid, brassinosteroids, and nitric oxide has been highlighted. Development of plant genotypes with restricted Cd uptake and reduced accumulation in edible portions by conventional and marker-assisted breeding are also presented. In this regard, use of molecular techniques including identification of QTLs, CRISPR/Cas9, and functional genomics to enhance the adverse impacts of Cd in plants may be quite helpful. The review’s results should aid in the development of novel and suitable solutions for limiting Cd bioavailability and toxicity, as well as the long-term management of Cd-polluted soils, therefore reducing environmental and human health hazards.

/pdf/cadmium-phytotoxicity-tolerance-and-advanced-remediation-qk8hkw71.pdf

Cadmium Phytotoxicity, Tolerance, and Advanced Remediation Approaches in Agricultural Soils; A Comprehensive Review

Uncovering the genetic basis of agronomic traits in wheat landraces is important for ensuring global food security via the development of improved varieties. Here, 723 wheat landraces from 10 Chinese agro-ecological zones were evaluated for 23 agronomic traits in six environments. All accessions could be clustered into five subgroups based on phenotypic data via discriminant function analysis, which was highly consistent with genotypic classification. A genome-wide association study was conducted for these traits using 52 303 DArT-seq markers to identify marker-trait associations and candidate genes. Using both the general linear model and the mixed linear model, 149 significant markers were identified for 21 agronomic traits based on best linear unbiased prediction values. Considering the linkage disequilibrium decay distance in this study, significant markers within 10 cM were combined as a quantitative trait locus (QTL), with a total of 29 QTL identified for 15 traits. Of these, five QTL for heading date, flag leaf width, peduncle length, and thousand kernel weight had been reported previously. Twenty-five candidate genes associated with significant markers were identified. These included the known vernalization genes VRN-B1 and vrn-B3 and the photoperiod response genes Ppd and PRR. Overall, this study should be helpful in elucidating the underlying genetic mechanisms of complex agronomic traits and performing marker-assisted selection in wheat.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.13614

A genome-wide association study of 23 agronomic traits in Chinese wheat landraces.

Aegilops tauschii is the D-genome progenitor of hexaploid wheat (Triticum aestivum). It is considered to be an important source of genetic variation for wheat breeding, and its genome is an invaluable reference for wheat genomics. We conducted a genome-wide association study using 7,185 single nucleotide polymorphism (SNP) markers across 322 diverse accessions of Ae. tauschii that were systematically phenotyped for 29 morphological traits in order to identify marker-trait associations and candidate genes, assess genetic diversity, and classify the accessions based on phenotypic data and genotypic comparison. Using the general linear model and mixed linear model, we identified a total of 18 SNPs significantly associated with 10 morphological traits. Systematic search of the flanking sequences of trait-associated SNPs in public databases identified several genes that may be linked to variations in phenotypes. Cluster analysis using phenotypic data grouped accessions into four clusters, while accessions in the same cluster were not from the same Ae. tauschii subspecies or from the same area of origin. This work establishes a fundamental research platform for association studies in Ae. tauschii and also provides useful information for understanding the genetic mechanism of agronomic traits in wheat.

/pdf/genome-wide-association-study-of-29-morphological-traits-in-554v4xnpis.pdf

Genome-wide association study of 29 morphological traits in Aegilops tauschii.

Aegilops tauschii, as one of wheat wild relatives, possesses a wide range of resistance to biotic/abiotic factors. To better utilize and provide the genetic basis of breeding for improving phosphorus deficiency tolerance, large-scale screening for tolerant A. tauschii to phosphorus deficiency was conducted using hydroponic experiment. A total of 380 A. tauschii genotypes were used to evaluate their phosphorus deficiency tolerance using root system at seedling stage. The results indicate that compared to applied phosphorus condition, genetic variation of the tested traits among 380 A. tauschii genotypes was significant under non-applied phosphorus condition. Heritability estimates showed that root dry weight, shoot dry weight, and total dry weight is highly inheritable. Principal component (PC) analysis showed that first four PCs explained 81.387 % of total variation. S value and phosphorus deficiency tolerance index (PDTI) showed that all A. tauschii genotypes can be divided into three groups, high (17 %), moderate (58 %) and low (25 %) tolerance groups. Compared with other cultivated wheat using S value and PDTI, the top five tolerant A. tauschii genotypes have stronger ability of phosphorus deficiency tolerance than other cultivated wheat. In conclusion, we systematically evaluated large-scale A. tauschii genotypes, and 63 tolerant lines and some root traits used as selection criteria were selected. The top five tolerant A. tauschii genotypes have relative higher tolerance than other wheat, and can be further used for wheat genetic improvement and molecular breeding for abiotic stress tolerance.

Large-scale screening for Aegilops tauschii tolerant genotypes to phosphorus deficiency at seedling stage

Aegilops tauschii Ais a wild relative of common wheat ( Triticum aestivum ) and acts as an important resource of elite genes including genes for resistance to biotic and abiotic stresses To improve the cadmium (Cd) tolerance of wheat varieties using A  tauschii resources, we investigated the genetic variation of biomass-based Cd tolerance in 235 A  tauschii accessions treated with 0 (control) and 100 μmol L − 1 CdCl 2 (as Cd stress) Simultaneously, we performed a genomewide association study (GWAS) using a single-nucleotide polymorphism chip containing 7185 markers Six markers were found to be significantly associated with Cd tolerance by a general linear model and a mixed linear model These markers were close to several candidate/flanking genes associated with Cd tolerance according to results in public databases, including pdil5 - 1 , Acc - 1 , DME - 5A , TaAP2 - D , TaAP2 - B , Vrn - B1 , and FtsH - like protein gene The A  tauschii accessions were classified as high, moderate, and low Cd-tolerant according to a secondary index, the synthetic index (SI), in proportions of 9%, 57%, and 34%, respectively By the average SI, accessions from Afghanistan, Turkey, Azerbaijan, and Iran showed relatively high Cd tolerance

Genomewide association study of Aegilops tauschii traits under seedling-stage cadmium stress

Using GWAS, 13 significant SNPs distributed on six of the seven Aegilops tauschii chromosomes (all but 5D) were identified, and several candidate P-deficiency-responsive genes were proposed from searches of public databases. Aegilops tauschii, the wheat (Triticum aestivum) D-genome progenitor, possesses numerous genes for stress resistance, including genes for tolerance of phosphorus (P) deficiency. Investigation of the genetic architecture of A. tauschii will help in developing P-deficiency-tolerant varieties of wheat. We evaluated nine traits in a population of 380 A. tauschii specimens under conditions with and without P application, and we performed genome-wide association studies for these traits using single nucleotide polymorphism (SNP) chips containing 7185 markers. Using a general linear model, we identified 119 SNPs that were significantly associated with all nine traits, and a mixed linear model revealed 18 SNPs associated with all traits. Both models detected 13 significant markers distributed on six of the seven A. tauschii chromosomes (all but 5D). Searches of public databases revealed several candidate/flanking genes related to P-deficiency tolerance. These genes were grouped in five categories by the types of proteins they encoded: defense response proteins, enzymes, promoters and transcription factors, storage proteins, or proteins triggered by P deficiency. The identified SNPs and genes contain essential information for cloning genes related to P-deficiency tolerance in A. tauschii and wheat, and they provide a foundation for breeding P-deficiency tolerant wheat cultivars.

Genome-wide association study of phosphorus-deficiency-tolerance traits in Aegilops tauschii

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Genome-wide association study of 29 morphological traits in Aegilops tauschii.

Large-scale screening for Aegilops tauschii tolerant genotypes to phosphorus deficiency at seedling stage

Genomewide association study of Aegilops tauschii traits under seedling-stage cadmium stress

Genome-wide association study of phosphorus-deficiency-tolerance traits in Aegilops tauschii