Multiparent Advanced Generation Intercross Research Articles

QTL identification for salt tolerance related traits at the seedling stage in indica rice using a multi-parent advanced generation intercross (MAGIC) population

Salinity is one of the most important abiotic stresses, which seriously affects rice production. In this study, a multiparent advanced generation intercross population, DC1, derived from intercrossing four elite indica varieties, was used to identify QTLs conferring salt tolerance. The whole population and four parents were genotyped with a 55K rice SNP array. A total of 7 QTLs delineated from 186 significant marker-trait associations were detected on chromosomes 1, 2, 5 and 9, which accounted for 7.42–9.38% of the total phenotypic variations. Among these QTLs, one novel QTL (qRRL2) on chromosome 2 for relative root length and one multi-trait QTL (qSLST1/qRDSW1/qRB1) on chromosome 1 affecting shoot length, root dry weight and root biomass under salt treatment were detected. Gene expression analysis revealed that a transcription factor gene (LOC_Os01g66280) within the multi-trait QTL is the potential candidate gene for salt tolerance. Interestingly, we identified one significant nonsynonymous SNP in the coding region of this candidate gene. These results will facilitate fine mapping of the candidate gene and QTL pyramiding to genetically improve salt tolerance in rice.

Resistance and susceptibility QTL identified in a rice MAGIC population by screening with a minor-effect virulence factor from Xanthomonas oryzae pv. oryzae.

SummaryEffective and durable disease resistance for bacterial blight (BB) of rice is a continuous challenge due to the evolution and adaptation of the pathogen, Xanthomonas oryzae pv. oryzae (Xoo), on cultivated rice varieties. Fundamental to this pathogens’ virulence is transcription activator‐like (TAL) effectors that activate transcription of host genes and contribute differently to pathogen virulence, fitness or both. Host plant resistance is predicted to be more durable if directed at strategic virulence factors that impact both pathogen virulence and fitness. We characterized Tal7b, a minor‐effect virulence factor that contributes incrementally to pathogen virulence in rice, is a fitness factor to the pathogen and is widely present in geographically diverse strains of Xoo. To identify sources of resistance to this conserved effector, we used a highly virulent strain carrying a plasmid borne copy of Tal7b to screen an indica multi‐parent advanced generation inter‐cross (MAGIC) population. Of 18 QTL revealed by genome‐wide association studies and interval mapping analysis, six were specific to Tal7b (qBB‐tal7b). Overall, 150 predicted Tal7b gene targets overlapped with qBB‐tal7b QTL. Of these, 21 showed polymorphisms in the predicted effector binding element (EBE) site and 23 lost the EBE sequence altogether. Inoculation and bioinformatics studies suggest that the Tal7b target in one of the Tal7b‐specific QTL, qBB‐tal7b‐8, is a disease susceptibility gene and that the resistance mechanism for this locus may be through loss of susceptibility. Our work demonstrates that minor‐effect virulence factors significantly contribute to disease and provide a potential new approach to identify effective disease resistance.

Abstract A45: Diet-induced obesity and caloric restriction weight loss in Diversity Outbred (DO) mice: An experimental preclinical translational model for the investigation of pathways for prevention of obesity and cancer

Abstract Obesity has reached epidemic levels worldwide. It is associated with major chronic diseases, including cancer and cardiovascular disease. The etiology of obesity-associated cancer is poorly understood. New population-based research mouse models are required to better understand prevention and to increase the translational potential of mouse models to humans. The Collaborative Cross (CC) recombinant inbred lines of mice are a population-based model created from an 8-way multiparental advanced generation intercross with a 12% minor allele frequency (MAF) and more than 45 million SNP and CNV, including a significant number of private (unique) alleles. The Diversity Outbred (DO) mice were created from early CC incipient lines (generations G2:F2-5) by random selection and 175 randomly selected breeding pairs. The genetic diversity of the DO and CC RIL mice is ideal for forward and reverse genetics approaches, respectively, to identify potential causally related risk variants and identify etiology based upon causal relationships. Here, we present data from two cohorts (from different breeding generations) of 50 female and 50 male DO mice each (total 100 each sex). After 12-wks high-fat (60% kcal fat) diet we observed significant differences in weight gain during diet-induced obesity DIO. After switching diets for 8-wks of 30% caloric restriction of a low-fat (10% kcal fat) diet, we observed significant interindividual differences in weight loss. Body weight, lean and fat mass differences), increases in 4-hr fasted blood glucose and insulin levels, insulin resistance (HOMA-IR and increased blood branched chain amino acids levels (BCAA) were observed. Four interacting quantitative trait loci/gene (Chst10, Bmiq5, Ath8, and Tcq14) related to metabolism, body mass index, cardiovascular disease, and total cholesterol levels, respectively, have been identified. Regression analysis suggests significant interactions between fasted blood glucose and fat mass, HOMA-IR and fat mass, and BCAA and fat mass in DIO and CR outcomes. Results to date show significant amounts of interindividual variability of each of the quantified phenotypes in response to both diet interventions were demonstrated in female and male DO mice. These data suggest potential avenues of research on obesity and cancer relationships and pathways for intervention. Citation Format: Melissa VerHague, Jody Albright, Salvador Favela, Kerri Barron, Michael F. Coleman, Katie Meyer, John E. French, Stephen D. Hursting. Diet-induced obesity and caloric restriction weight loss in Diversity Outbred (DO) mice: An experimental preclinical translational model for the investigation of pathways for prevention of obesity and cancer [abstract]. In: Proceedings of the AACR Special Conference on Environmental Carcinogenesis: Potential Pathway to Cancer Prevention; 2019 Jun 22-24; Charlotte, NC. Philadelphia (PA): AACR; Can Prev Res 2020;13(7 Suppl): Abstract nr A45.

Genetic dissection of the interactions between semi-dwarfing genes sdw1 and ari-e and their effects on agronomic traits in a barley MAGIC population

The introduction of semi-dwarf cereal crop varieties in the 1960s enabled extensive increases in global food production. Semi-dwarf barley cultivars have shorter stature and improved stress resistance, grain yield and quality than tall varieties. The major semi-dwarf genes, sdw1 and ari-e, have been widely used in barley breeding programmes worldwide. In this study, we identified a novel sdw1 allele in cv. Lockyer and investigated the effect of sdw1 and ari-e and their interactions on plant height, flowering time and grain yield using a Multi-parent Advanced Generation Inter-cross (MAGIC) population generated from four elite barley cultivars. Allele-specific markers combined with Kompetitive Allele Specific Polymerase Chain Reaction (KASP) assays were used for fast and accurate screening of plants with different allele combinations. The results showed that the novel sdw1 allele from cv. Lockyer had similar effects on plant growth and phenology as the known sdw1.d allele. The two semi-dwarf genes sdw1 and ari-e had an additive effect for plant height with height reductions up to 27 cm. The ari-e gene triggered earlier flowering up to 6 days compared to WT and reduced the delay in flowering time caused by the sdw1 gene. The two semi-dwarf genes boosted grain yields by 20% in the sdw1 plants and up to 28% in plants with the two combined semi-dwarf genes. The results presented will benefit the development of higher-yielding and better-adapted barley cultivars.

Genetic basis of phenotypic plasticity and genotype × environment interactions in a multi-parental tomato population.

Deciphering the genetic basis of phenotypic plasticity and genotype × environment interactions (G×E) is of primary importance for plant breeding in the context of global climate change. Tomato (Solanum lycopersicum) is a widely cultivated crop that can grow in different geographical habitats and that displays a great capacity for expressing phenotypic plasticity. We used a multi-parental advanced generation intercross (MAGIC) tomato population to explore G×E and plasticity for multiple traits measured in a multi-environment trial (MET) comprising optimal cultural conditions together with water deficit, salinity, and heat stress over 12 environments. Substantial G×E was observed for all the traits measured. Different plasticity parameters were estimated by employing Finlay-Wilkinson and factorial regression models and these were used together with genotypic means for quantitative trait loci (QTL) mapping analyses. In addition, mixed linear models were also used to investigate the presence of QTL × environment interactions. The results highlighted a complex genetic architecture of tomato plasticity and G×E. Candidate genes that might be involved in the occurrence of G×E are proposed, paving the way for functional characterization of stress response genes in tomato and for breeding climate-adapted cultivars.

Ms3 dominant genetic male sterility for wheat improvement with molecular breeding

AbstractGenetic dominant male sterility (DMS) has not been widely used as a breeding tool in wheat (Triticum aestivum L.), although DMS‐facilitated backcross, mass selection, half‐sib selection, and S1 family recurrent selection strategies have been described, and Ms2‐facilitated recurrent selection has been used in China. Our objective was to revisit these strategies using the tools of molecular breeding. Development of a mechanism for seedling identification of sterile progeny was a key component of designing practical DMS‐facilitated molecular breeding systems. The DMS gene Ms3 was previously localized to the centromeric region of chromosome 5A. The centromeric location is an advantage because recombination rates are very low. Once identified, a broadly informative marker would reliably predict the male‐sterile phenotype. A set of 429 hybrids incorporating Ms3 were constructed, both within US hard winter wheats, and between these winter wheats and Asian spring wheats. Association of the male‐sterile phenotype with those polymorphic DNA sequence tags that localized to chromosome 5A was tested using case‐control association analysis. Two highly significant (logarithm of odds [LOD] > 30) single nucleotide polymorphism (SNP)–trait associations were obtained. One SNP was developed into a highly sensitive, reliable marker for the Ms3‐associated male‐sterile phenotype. Previously described breeding strategies using DMS were updated for trait‐targeted marker‐assisted backcrossing and gene pyramiding, S1 recurrent selection, and early‐generation genomic selection. Application of DMS to association mapping, with the particular use case of the multiparent advanced generation intercross population, is also described.

Genome-Wide Association Study of Grain Size Traits in Indica Rice Multiparent Advanced Generation Intercross (MAGIC) Population.

Rice grain size plays a crucial role in determining grain quality and yield. In this study, two multiparent advanced generation intercross (MAGIC) populations, DC1 and BIM, were evaluated for grain size across three environments and genotyped with 55K array-based SNP detection and genotype-by-sequencing (GBS), respectively, to identify QTLs and SNPs associated with grain length, grain width, grain length–width ratio, grain thickness, and thousand grain weight. A total of 18 QTLs were identified for the five grain size-related traits and explained 6.43–63.35% of the total phenotypic variance. Twelve of these QTLs colocalized with the cloned genes, GS3, GW5/qSW5, GW7/GL7/SLG7, and GW8/OsSPL16, of which the first two genes showed the strongest effect for grain length and grain width, respectively. Four potential new genes were also identified from the QTLs, which exhibited both genetic background independency and environment stability and could be validated in future studies. Moreover, the significant SNP markers identified are valuable for direct utilization in marker-assisted breeding to improve rice grain size.

Identification and Quantitation of Amylase Trypsin Inhibitors Across Cultivars Representing the Diversity of Bread Wheat.

α-Amylase/trypsin inhibitors (ATIs) may have a role in nonceliac wheat sensitivity (NCWS) and celiac disease (CD), but the ATI content and diversity across a range of wheat cultivars are not well characterized. Discovery proteomics was used to detect ATIs across two wheat cultivars: Chara and Magenta. Comprehensive mapping of detected ATIs with the ATIs from the recently published wheat genome RefSeq v1.0 shows the presence of three major subclasses: monomeric (9%), dimeric (61%), and chloroform-methanol (CM) type (30%). Subsequently, the level of 18 ATI isoforms (63 peptides) grouped into four subtypes was monitored across 15 commercial wheat cultivars and the eight parental lines from a multiparent advanced-generation intercross (MAGIC) population using liquid chromatography-multiple reaction monitoring-mass spectrometry (LC-MRM-MS). The ATI content of wheat cultivars Janz, Sunvale, Diamond Bird, and Longreach Scout was significantly lower than that of other wheat cultivars. The MAGIC parental cultivars Baxter and Xiaoyan 54 contain higher levels (∼115% relative to the average wheat ATI content), whereas cultivar Pastor contained the lowest levels (∼87%). Comprehensive sequence analysis, annotation, chromosomal locations, and epitope mapping enabled us to build an LC-MRM-MS method to monitor and quantify the immunostimulatory ATI proteins potentially related to NCWS, autoimmune diseases, and metabolic disorders. This provides an opportunity to select wheat cultivars with significantly lower levels of ATIs.

Recombination Pattern Characterization via Simulation Using Different Maize Populations.

Efficient recombination is critical to both plant breeding and gene cloning. However, almost all traditional recombination studies and genetic improvements require the slow and labor-intensive population construction process, and little is known about the recombination characteristics of populations of different types, generations, and origins. Here, we provide a simple and efficient simulation method for population construction based on doubled haploid (DH) and intermated B73 × Mo17 maize (IBM) populations to predict the recombination pattern. We found that the chromosomes had 0, 1, 2, and 3 recombination events that occurred at rates of 0.16, 0.30, 0.23, and 0.15, respectively, in the DH and the recombination rate of each chromosome in the IBM population ranged from 0 to 12.1 cM per 125 kb. Based on the observed recombination parameters, we estimated the number of recombination events and constructed the linkage maps of the simulated DH and recombination inbred line (RIL) populations. These simulated populations exhibited similar recombination patterns compared with the real populations, suggesting the feasibility of this simulation approach. We then compared the recombination rates of the simulated populations of different types (DH induced or self-crossed), generations, and origins (using the 8, 16, and 32 multiparent advanced generation intercross (MAGIC) populations), and suggested a rapid and cost-effective population construction procedure for breeders and geneticists, while maintaining an optimal recombination rate. This study offers a convenient method for optimizing the population construction process and has broader implications for other crop species, thereby facilitating future population studies and genetic improvement strategies.

Mapping and validation of a fiber length QTL on chromosome D11 using two independent F2 populations of upland cotton

The analysis of association between genotypic markers and phenotypic traits allows identification of quantitative trait loci (QTLs), which can be applied through marker-assisted selection in breeding programs to improve the quality of crops. However, success in these applications depends primarily on the stability and dominance of the QTL. We previously identified a significant fiber length (FL) QTL on chromosome (Chr.) D11 based on the genome-wide association study (GWAS) of a multi-parent advanced generation inter-cross (MAGIC) population in upland cotton. In this report, we conducted mapping studies with two bi-parental populations to confirm the stability of the FL QTL on Chr. D11 and determine the magnitude of its effect on the fiber length phenotype. One of the F2 populations was developed from a cross between the longest fiber and the shortest fiber recombinant inbred lines (RILs) of the MAGIC population originally used for GWAS, whereas the second F2 population was created from a cross between two cotton lines Acala 1517–80 and JJ1145ne, which were not among the eleven MAGIC parental lines. The populations were grown in different environmental conditions. Genetic mapping of these populations confirmed the stability of the FL QTL on Chr. D11. The highest LOD scores of association with fiber length in both populations showed three SNP markers that resided within 360 kb of the QTL region on Chr. D11. Ten genes possessing non synonymous SNPs (nsSNPs) in their protein coding regions were identified in this region. RNAseq analysis detected activity in developing fiber tissue for seven of these candidate genes.

Genetic mapping using a wheat multi-founder population reveals a locus on chromosome 2A controlling resistance to both leaf and glume blotch caused by the necrotrophic fungal pathogen Parastagonospora nodorum

Key messageA locus on wheat chromosome 2A was found to control field resistance to both leaf and glume blotch caused by the necrotrophic fungal pathogen Parastagonospora nodorum.The necrotrophic fungal pathogen Parastagonospora nodorum is the causal agent of Septoria nodorum leaf blotch and glume blotch, which are common wheat (Triticum aestivum L.) diseases in humid and temperate areas. Susceptibility to Septoria nodorum leaf blotch can partly be explained by sensitivity to corresponding P. nodorum necrotrophic effectors (NEs). Susceptibility to glume blotch is also quantitative; however, the underlying genetics have not been studied in detail. Here, we genetically map resistance/susceptibility loci to leaf and glume blotch using an eight-founder wheat multiparent advanced generation intercross population. The population was assessed in six field trials across two sites and 4 years. Seedling infiltration and inoculation assays using three P. nodorum isolates were also carried out, in order to compare quantitative trait loci (QTL) identified under controlled conditions with those identified in the field. Three significant field resistance QTL were identified on chromosomes 2A and 6A, while four significant seedling resistance QTL were detected on chromosomes 2D, 5B and 7D. Among these, QSnb.niab-2A.3 for field resistance to both leaf blotch and glume blotch was detected in Norway and the UK. Colocation with a QTL for seedling reactions against culture filtrate from a Norwegian P. nodorum isolate indicated the QTL could be caused by a novel NE sensitivity. The consistency of this QTL for leaf blotch at the seedling and adult plant stages and culture filtrate infiltration was confirmed by haplotype analysis. However, opposite effects for the leaf blotch and glume blotch reactions suggest that different genetic mechanisms may be involved.

Genetic analysis of wheat sensitivity to the ToxB fungal effector from Pyrenophora tritici-repentis, the causal agent of tan spot

Key messageGenetic mapping of sensitivity to the Pyrenophora tritici-repentis effector ToxB allowed development of a diagnostic genetic marker, and investigation of wheat pedigrees allowed transmission of sensitive alleles to be tracked.Tan spot, caused by the necrotrophic fungal pathogen Pyrenophora tritici-repentis, is a major disease of wheat (Triticum aestivum). Secretion of the P. tritici-repentis effector ToxB is thought to play a part in mediating infection, causing chlorosis of plant tissue. Here, genetic analysis using an association mapping panel (n = 480) and a multiparent advanced generation intercross (MAGIC) population (n founders = 8, n progeny = 643) genotyped with a 90,000 feature single nucleotide polymorphism (SNP) array found ToxB sensitivity to be highly heritable (h2 ≥ 0.9), controlled predominantly by the Tsc2 locus on chromosome 2B. Genetic mapping of Tsc2 delineated a 1921-kb interval containing 104 genes in the reference genome of ToxB-insensitive variety ‘Chinese Spring’. This allowed development of a co-dominant genetic marker for Tsc2 allelic state, diagnostic for ToxB sensitivity in the association mapping panel. Phenotypic and genotypic analysis in a panel of wheat varieties post-dated the association mapping panel further supported the diagnostic nature of the marker. Combining ToxB phenotype and genotypic data with wheat pedigree datasets allowed historic sources of ToxB sensitivity to be tracked, finding the variety ‘Maris Dove’ to likely be the historic source of sensitive Tsc2 alleles in the wheat germplasm surveyed. Exploration of the Tsc2 region gene space in the ToxB-sensitive line ‘Synthetic W7984’ identified candidate genes for future investigation. Additionally, a minor ToxB sensitivity QTL was identified on chromosome 2A. The resources presented here will be of immediate use for marker-assisted selection for ToxB insensitivity and the development of germplasm with additional genetic recombination within the Tsc2 region.

Evaluation and genome-wide association study of Verticillium wilt resistance in a MAGIC population derived from intermating of eleven Upland cotton (Gossypium hirsutum) parents

Vertcillium wilt (VW, Verticillium dahliae Kleb.) is one of the most important soil-borne fungal diseases affecting world cotton production. Numerous studies have been conducted to investigate the genetic basis of VW resistance using bi-parental or association mapping populations. In this study, a multi-parent advanced generation inter-cross (MAGIC) population of 550 recombinant inbred lines (RILs) together with their 11 Upland cotton parents with a total of 473,516 polymorphic SNP markers was used to identify chromosomal regions for VW resistance based on foliar disease severity ratings (DSR) in two replicated greenhouse tests. Among the 11 parents, Acala Ultima, Coker 315, and Deltapine Acala 90 in the two tests and FiberMax 966 in one test and on average were significantly more resistant than the susceptible check parent- Phytogen PSC 355, while Paymaster HS 26, SureGrow 747, Stoneville 474, Stoneville 825, and Tamcot Pyramid performed similarly to PSC 355. Although a significant genotype × test interaction was detected for DSR, 37 MAGIC lines were consistently resistant to VW. Of 13 and 12 VW resistance QTL declared in Test 1 and 2, respectively, through a genome-wide association study (GWAS), three QTL on chromosome A01, D02 and D08 were in common and three QTL clusters were detected on chromosome A01, A13, and D01 between the two tests. The narrow chromosomal regions for the three common resistance QTL allowed identification of possible candidate genes for VW resistance. This greenhouse study identified VW resistant parents and RILs and common resistance QTL for VW resistance, providing useful information for developing VW resistant cultivars and further genomic studies towards the identification of VW resistance genes in cotton.

Dissecting the genetics of cold tolerance in a multiparental maize population.

We identify the largest amount of QTLs for cold tolerance in maize; mainly associated with photosynthetic efficiency, which opens new possibilities for genomic selection for cold tolerance in maize. Breeding for cold tolerance in maize is an important objective in temperate areas. The objective was to carry out a highly efficient study of quantitative trait loci (QTLs) for cold tolerance in maize. We evaluated 406 recombinant inbred lines from a multi-parent advanced generation intercross (MAGIC) population in a growth chamber under cold and control conditions, and in the field at early and normal sowing. We recorded cold tolerance-related traits, including the number of days from sowing to emergence, chlorophyll content and maximum quantum efficiency of photosystem II (Fv/Fm). Association mapping was based on genotyping with near one million single nucleotide polymorphism (SNP) markers. We found 858 SNPs significantly associated with all traits, most of them under cold conditions and early sowing. Most QTLs were associated with chlorophyll and Fv/Fm. Many candidate genes coincided between the current research and previous reports. These results suggest that (1) the MAGIC population is an efficient tool for identifying QTLs for cold tolerance; (2) most QTLs for cold tolerance were associated with Fv/Fm; (3) most of these QTLs were located in specific genomic regions, particularly bin 10.04; (4) the current study allows genetically improving cold tolerance with genome-wide selection.

Mapping of resistance to corn borers in a MAGIC population of maize

BackgroundCorn borers constitute an important pest of maize around the world; in particular Sesamia nonagrioides Lefèbvre, named Mediterranean corn borer (MCB), causes important losses in Southern Europe. Methods of selection can be combined with transgenic approaches to increase the efficiency and durability of the resistance to corn borers. Previous studies of the genetic factors involved in resistance to MCB have been carried out using bi-parental populations that have low resolution or using association inbred panels that have a low power to detect rare alleles. We developed a Multi-parent Advanced Generation InterCrosses (MAGIC) population to map with high resolution the genetic determinants of resistance to MCB.ResultsWe detected multiple single nucleotide polymorphisms (SNPs) of low effect associated with resistance to stalk tunneling by MCB. We dissected a wide region related to stalk tunneling in multiple studies into three smaller regions (at ~ 150, ~ 155, and ~ 165 Mb in chromosome 6) that closely overlap with regions associated with cell wall composition. We also detected regions associated with kernel resistance and agronomic traits, although the co-localization of significant regions between traits was very low. This indicates that it is possible the concurrent improvement of resistance and agronomic traits.ConclusionsWe developed a mapping population which allowed a finer dissection of the genetics of maize resistance to corn borers and a solid nomination of candidate genes based on functional information. The population, given its large variability, was also adequate to map multiple traits and study the relationship between them.

Whole-Genome Resequencing of Seven Eggplant (Solanum melongena) and One Wild Relative (S. incanum) Accessions Provides New Insights and Breeding Tools for Eggplant Enhancement.

Whole-genome resequencing provides information of great relevance for crop genetics, evolution, and breeding. Here, we present the first whole-genome resequencing study using seven eggplant (Solanum melongena) and one wild relative (Solanum incanum) accessions. These eight accessions were selected for displaying a high phenotypic and genetic diversity and for being the founder parents of an eggplant multiparent advanced generation intercrosses population. By resequencing at an average depth of 19.8× and comparing to the high-quality reference genome “67/3” over 10 million high-reliable polymorphisms were discovered, of which over 9 million (84.5%) were single nucleotide polymorphisms and more than 700,000 (6.5%) InDels. However, while for the S. melongena accessions, the variants identified ranged from 0.8 to 1.3 million, over 9 million were detected for the wild S. incanum. This confirms the narrow genetic diversity of the domesticated eggplant and suggests that introgression breeding using wild relatives can efficiently contribute to broadening the genetic basis of this crop. Differences were observed among accessions for the enrichment in genes regulating important biological processes. By analyzing the distribution of the variants, we identified the potential footprints of old introgressions from wild relatives that can help to unravel the unclear domestication and breeding history. The comprehensive annotation of these eight genomes and the information provided in this study represents a landmark in eggplant genomics and allows the development of tools for eggplant genetics and breeding.

Bin-based genome-wide association analyses improve power and resolution in QTL mapping and identify favorable alleles from multiple parents in a four-way MAGIC rice population.

A whole genome bin map was developed for a MAGIC population. Association studies for heading date at bin level exhibited powerful QTL mapping and identified favorable alleles. The presumed advantages of multiparent advanced generation intercross (MAGIC) population in quantitative trait locus (QTL) mapping were not fully utilized in the previous studies in which genome-wide association studies (GWAS) were conducted at only single nucleotide polymorphism level. In this study, we genotyped a rice four-way MAGIC population of 247 F7 lines and their parents by sequencing. A total of 5934 bins with an average length of 65kb were constructed and covered 97% of the genome. The MAGIC population showed low population structure and balanced parental contributions. A bin-based GWAS for heading date identified 4 QTLs in three environments. Three major QTLs were mapped exactly to the bins where the major heading date genes DTH3, Ghd7.1 and Ghd8 were located. Multiple comparisons showed that different parental alleles had varied genetic effects. Like DTH3, the alleles of the Guichao 2/YJSM, IR34 and Cypress had larger, intermediate and no effects, respectively. Based on comparative sequencing of 8 known heading date genes undetected in this MAGIC population, only Ghd7 exhibited diverse function among parents. The failure in Ghd7 mapping was well explained by its interaction with Hd1 because Ghd7 had no effects on heading date when combined with the nonfunctional hd1 carried by all four parents. Overall, bin-based GWAS have more mapping power and higher resolution with a MAGIC population and provide favorable alleles to breeders. The use of more diversified parents is encouraged to develop a MAGIC population for detecting more QTLs for important agronomical traits.

What five insects told us about how a native plant copes with real-world problems

What five insects told us about how a native plant copes with real-world problems

Wheat grain number and yield: The relative importance of physiological traits and source-sink balance in southern Australia

Grain number (GN) is determined by spike growth rate (SGR), fruiting efficiency (FE) and the duration of spike growth period (Ds). However, these three traits are not independent of each other and therefore quantifying their relative contribution to GN is important for improving yield potential. This study aimed to model GN as a function of SGR, FE and Ds in bread wheat and investigate the relative importance of these three traits in determining GN. A large number of commercial varieties, elite wheat breeding lines, and a Multiparent Advanced Generation InterCross population were evaluated for GN, SGR, Ds, and FE in six Australian environments in 2014 and 2015. The model explained 43–98% of the variation in GN in individual environments and 88% of the variation in GN across the six environments. The percentage of GN variance explained by the model was significantly higher than those explained by correlating GN to individual traits. The relative importance of the contribution of the three traits to GN was different and ranked as SGR > FE > Ds. The negative correlation between FE and spike dry weight at anthesis (SDWa) appears to be spurious, suggesting that there was no causality between high FE and low SDWa and vice versa. Thus, FE can be used as an independent trait to increase GN in addition to SGR and Ds. We also investigated if the wheat crop had enough source to fill the increased sink size in the southern Australian high rainfall environment. The source-sink balance analysis indicates that the available source, consisting of concurrent photosynthetic assimilate and stored water-soluble carbohydrate at anthesis, was sufficient to fill the established sink but no surplus assimilates were available to fill a larger sink in southwestern Australia. However, the opportunity to increase yield potential by further increasing grain number might exist in south-eastern Australia environments.

Epistasis Detection and Modeling for Genomic Selection in Cowpea (Vigna unguiculata L. Walp.).

Genetic architecture reflects the pattern of effects and interaction of genes underlying phenotypic variation. Most mapping and breeding approaches generally consider the additive part of variation but offer limited knowledge on the benefits of epistasis which explains in part the variation observed in traits. In this study, the cowpea multiparent advanced generation inter-cross (MAGIC) population was used to characterize the epistatic genetic architecture of flowering time, maturity, and seed size. In addition, consideration for epistatic genetic architecture in genomic-enabled breeding (GEB) was investigated using parametric, semi-parametric, and non-parametric genomic selection (GS) models. Our results showed that large and moderate effect–sized two-way epistatic interactions underlie the traits examined. Flowering time QTL colocalized with cowpea putative orthologs of Arabidopsis thaliana and Glycine max genes like PHYTOCLOCK1 (PCL1 [Vigun11g157600]) and PHYTOCHROME A (PHY A [Vigun01g205500]). Flowering time adaptation to long and short photoperiod was found to be controlled by distinct and common main and epistatic loci. Parametric and semi-parametric GS models outperformed non-parametric GS model, while using known quantitative trait nucleotide(s) (QTNs) as fixed effects improved prediction accuracy when traits were controlled by large effect loci. In general, our study demonstrated that prior understanding of the genetic architecture of a trait can help make informed decisions in GEB.