Dissection of maize kernel composition and starch production by candidate gene association

Identification of superior haplotypes for flowering time in pigeonpea through candidate gene-based association study of a diverse minicore collection

KEY MESSAGE

In current study candidate gene (261 genes) based association mapping on 144 pigeonpea accessions for flowering time and related traits and 29 MTAs producing eight superior haplotypes were identified. In the current study, we have conducted an association analysis for flowering-associated traits in a diverse pigeonpea mini-core collection comprising 144 accessions using the SNP data of 261 flowering-related genes. In total, 13,449 SNPs were detected in the current study, which ranged from 743 (ICP10228) to 1469 (ICP6668) among the individuals. The nucleotide diversity (0.28) and Watterson estimates (0.34) reflected substantial diversity, while Tajima's D (-0.70) indicated the abundance of rare alleles in the collection. A total of 29 marker trait associations (MTAs) were identified, among which 19 were unique to days to first flowering (DOF) and/or days to fifty percent flowering (DFF), 9 to plant height (PH), and 1 to determinate (Det) growth habit using 3 years of phenotypic data. Among these MTAs, six were common to DOF and/or DFF, and four were common to DOF/DFF along with the PH, reflecting their pleiotropic action. These 29 MTAs spanned 25 genes, among which 10 genes clustered in the protein-protein network analysis, indicating their concerted involvement in floral induction. Furthermore, we identified eight haplotypes, four of which regulate late flowering, while the remaining four regulate early flowering using the MTAs. Interestingly, haplotypes conferring late flowering (H001, H002, and H008) were found to be taller, while those involved in early flowering (H003) were shorter in height. The expression pattern of these genes, as inferred from the transcriptome data, also underpinned their involvement in floral induction. The haplotypes identified will be highly useful to the pigeonpea breeding community for haplotype-based breeding.

Revisiting maize Brittle endosperm-2 reveals new insights in BETL development and starchy endosperm filling

Rerouting the starch biosynthesis pathway in maize can generate specialty types, like sweet corn and waxy corn, with a drastically increasing global demand. Hence, a fine-tuning of starch metabolism is relevant to create diverse maize cultivars for end-use applications. Here, we characterized a new maize brittle endosperm mutant, referred to as bt1774, which exhibited decreased starch content but a dramatic increase of soluble sugars at maturity. Both endosperm and embryo development was impaired in bt1774 relative to the wild-type (WT), with a prominently arrested basal endosperm transfer layer (BETL). Map-based cloning revealed that BRITTLE ENDOSPERM2 (Bt2), which encodes a small subunit of ADP-glucose pyrophosphorylase (AGPase), is the causal gene for bt1774. A MuA2 element was found to be inserted into intron 2 of Bt2, leading to a severe decrease of its expression, in bt1774. This is in line with the irregular and loosely packed starch granules in the mutant. Transcriptome of endosperm at grain filling stage identified 1, 013 differentially expressed genes in bt1774, which were notably enriched in the BETL compartment, including ZmMRP1, Miniature1, MEG1, and BETLs. Gene expression of the canonical starch biosynthesis pathway was marginally disturbed in Bt1774. Combined with the residual 60% of starch in this nearly null mutant of Bt2, this data strongly suggests that an AGPase-independent pathway compensates for starch synthesis in the endosperm. Consistent with the BETL defects, zein accumulation was impaired in bt1774. Co-expression network analysis revealed that Bt2 probably has a role in intracellular signal transduction, besides starch synthesis. Altogether, we propose that Bt2 is likely involved in carbohydrate flux and balance, thus regulating both the BETL development and the starchy endosperm filling.

Germplasm Resources and Strategy for Genetic Breeding of Lycium Species: A Review

Lycium species (goji), belonging to Solanaceae, are widely spread in the arid to semiarid environments of Eurasia, Africa, North and South America, among which most species have affinal drug and diet functions, resulting in their potential to be a superior healthy food. However, compared with other crop species, scientific research on breeding Lycium species lags behind. This review systematically introduces the present germplasm resources, cytological examination and molecular-assisted breeding progress in Lycium species. Introduction of the distribution of Lycium species around the world could facilitate germplasm collection for breeding. Karyotypes of different species could provide a feasibility analysis of fertility between species. The introduction of mapping technology has discussed strategies for quantitative trait locus (QTL) mapping in Lycium species according to different kinds of traits. Moreover, to extend the number of traits and standardize the protocols of trait detection, we also provide 1,145 potential traits (275 agronomic and 870 metabolic) in different organs based on different reference studies on Lycium, tomato and other Solanaceae species. Finally, perspectives on goji breeding research are discussed and concluded. This review will provide breeders with new insights into breeding Lycium species.

New Techniques in Structural Tailoring of Starch Functionality

Inherent characteristics of native starches such as water insolubility, retrogradation and syneresis, and instability in harsh processing conditions (e.g., high temperature and shearing, low pH) limit their industrial applications. As starch properties mainly depend on starch composition and structure, structural tailoring of starch has been important for overcoming functional limitations and expanding starch applications in different fields. In this review, we first introduce the basics of starch structure, properties, and functionalities and then describe the interactions of starch with lipids, polysaccharides, and phenolics. After reviewing genetic, chemical, and enzymatic modifications of starch, we describe current progress in the areas of porous starch and starch-based nanoparticles. New techniques, such as using the CRISPR-Cas9 technique to tailor starch structures and using an emulsion-assisted approach in forming functional starch nanoparticles, are only feasible when they are established based on fundamental knowledge of starch. Expected final online publication date for the Annual Review of Food Science and Technology, Volume 13 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Association analysis of physiological traits in spring barley (Hordeum vulgare L.) under water-deficit conditions

In the present study, 148 commercial barley cultivars were assessed by 14 AFLP primer combinations and 32 SSRs primer pairs. Population structure, linkage disequilibrium, and genomic regions associated with physiological traits under drought stress were investigated. The phenotypic results showed a high level of diversity between studied cultivars. The studied barley cultivars were divided into two subgroups. Linkage disequilibrium analysis revealed that r 2 values among all possible marker pairs have an average value of 0.0178. The mixed linear model procedure showed that totally, 207 loci had a significant association with investigated traits. 120 QTLs out of 207 were detected for traits under normal conditions, and 90 QTLs were detected for traits under drought stress conditions. Identified QTLs after validation and transferring to SCAR markers in the case of AFLPs can be used to develop MAS strategies for barley breeding programs. Some common markers were identified for a particular trait or some traits across normal and drought stress conditions. These markers show low interaction with environmental conditions (stable markers); therefore, selection by them for a trait under normal conditions will improve the trait value under stress conditions, too.

Genome-wide association study reveals that different pathways contribute to grain quality variation in sorghum (Sorghum bicolor)

BACKGROUND

In sorghum (Sorghum bicolor), one paramount breeding objective is to increase grain quality. The nutritional quality and end use value of sorghum grains are primarily influenced by the proportions of tannins, starch and proteins, but the genetic basis of these grain quality traits remains largely unknown. This study aimed to dissect the natural variation of sorghum grain quality traits and identify the underpinning genetic loci by genome-wide association study.

RESULTS

Levels of starch, tannins and 17 amino acids were quantified in 196 diverse sorghum inbred lines, and 44 traits based on known metabolic pathways and biochemical interactions amongst the 17 amino acids calculated. A Genome-wide association study (GWAS) with 3,512,517 SNPs from re-sequencing data identified 14, 15 and 711 significant SNPs which represented 14, 14, 492 genetic loci associated with levels of tannins, starch and amino acids in sorghum grains, respectively. Amongst these significant SNPs, two SNPs were associated with tannin content on chromosome 4 and colocalized with three previously identified loci for Tannin1, and orthologs of Zm1 and TT16 genes. One SNP associated with starch content colocalized with sucrose phosphate synthase gene. Furthermore, homologues of opaque1 and opaque2 genes associated with amino acid content were identified. Using the KEGG pathway database, six and three candidate genes of tannins and starch were mapped into 12 and 3 metabolism pathways, respectively. Thirty-four candidate genes were mapped into 16 biosynthetic and catabolic pathways of amino acids. We finally reconstructed the biosynthetic pathways for aspartate and branched-chain amino acids based on 15 candidate genes identified in this study.

CONCLUSION

Promising candidate genes associated with grain quality traits have been identified in the present study. Some of them colocalized with previously identified genetic regions, but novel candidate genes involved in various metabolic pathways which influence grain quality traits have been dissected. Our study acts as an entry point for further validation studies to elucidate the complex mechanisms controlling grain quality traits such as tannins, starch and amino acids in sorghum.

Accelerating Breeding for Heat Tolerance in Tomato (Solanum lycopersicum L.): An Integrated Approach

Heat stress is a major limiting factor for crop productivity. Tomato is highly sensitive to heat stress, which can result in a total yield loss. To adapt to current and future heat stress, there is a dire need to develop heat tolerant cultivars. Here, we review recent attempts to improve screening for heat tolerance and to exploit genetic and genomic resources in tomatoes. We provide key factors related to phenotyping environments and traits (morphological, physiological, and metabolic) to be considered to identify and breed thermo-tolerant genotypes. There is significant variability in tomato germplasm that can be harnessed to breed for thermo-tolerance. Based on our review, we propose that the use of advanced backcross populations and chromosome segments substitution lines is the best means to exploit variability for heat tolerance in non-cultivated tomato species. We applied a meta quantitative trait loci (MQTL) analysis on data from four mapping experiments to co-localize QTL associated with heat tolerance traits (e.g., pollen viability, number of pollen, number of flowers, style protrusion, style length). The analysis revealed 13 MQTL of which 11 were composed of a cluster of QTL. Overall, there was a reduction of about 1.5-fold in the confidence interval (CI) of the MQTL (31.82 cM) compared to the average CI of individual QTL (47.4 cM). This confidence interval is still large and additional mapping resolution approaches such as association mapping and multi-parent linkage mapping are needed. Further investigations are required to decipher the genetic architecture of heat tolerance surrogate traits in tomatoes. Genomic selection and new breeding techniques including genome editing and speed breeding hold promise to fast-track development of improved heat tolerance and other farmer- and consumer-preferred traits in tomatoes.

Multi-dimensional evaluation of response to salt stress in wheat

Soil salinity is a major threat to crop production worldwide. The global climate change is further accelerating the process of soil salinization, particularly in dry areas of the world. Increasing genetic variability of currently used wheat varieties by introgression of exotic alleles/genes from related progenitors' species in breeding programs is an efficient approach to overcome limitations due to the absence of valuable genetic diversity in elite cultivars. Synthetic hexaploid wheat (SHW) is widely regarded as donor of favourable exotic alleles to improve tolerance against biotic and abiotic stresses such as salinity stress. In this study, synthetic backcross lines (SBLs) winter wheat population "Z86", derived from crosses involving synthetic hexaploid wheat Syn86L with German elite winter wheat cultivar Zentos, was evaluated for salinity tolerance at different developmental stages under controlled and field conditions in three growing seasons. High genetic variability was detected across the SBLs and their parents at various growth stages under controlled as well as under salt stress field trials. Greater performance of Zentos over Syn86L was detected at germination stage across all salt treatments and with respect to shoot dry weight (SDW) and root dry weight (RDW) at seedling stage. Whereas for the root length (RL) and the shoot length (SL) Syn86L surpassed the elite cultivar and most of the progenies. Our experiments revealed for almost all traits that some genotypes among the SBLs showed higher performance than their parents. Furthermore, positive transgressive segregations were detected among the SBLs for germination at high salinity levels, as well as for RDW and SDW at seedling stage. Therefore, the studied Z86 population is a suitable population for assessment of salinity stress on morphological and physiological traits at different plant growth stages. The identified SBLs provide a valuable source for genetic gain through recombination of superior alleles that can be directly applied in breeding programs for efficiently breeding cultivars with improved salinity tolerance and desired agronomic traits.

Linkage mapping and genome-wide association reveal candidate genes conferring thermotolerance of seed-set in maize

It is predicted that high-temperature stress will increasingly affect crop yields worldwide as a result of climate change. In order to determine the genetic basis of thermotolerance of seed-set in maize under field conditions, we performed mapping of quantitative trait loci (QTLs) in a recombinant inbred line (RIL) population using a collection of 8329 specifically developed high-density single-nucleotide polymorphism (SNP) markers, combined with a genome-wide association study (GWAS) of 261 diverse maize lines using 259 973 SNPs. In total, four QTLs and 17 genes associated with 42 SNPs related to thermotolerance of seed-set were identified. Among them, four candidate genes were found in both linkage mapping and GWAS. Thermotolerance of seed-set was increased significantly in near-isogenic lines (NILs) that incorporated the four candidate genes in a susceptible parent background. The expression profiles of two of the four genes showed that they were induced by high temperatures in the maize tassel in a tolerant parent background. Our results indicate that thermotolerance of maize seed-set is regulated by multiple genes each of which has minor effects, with calcium signaling playing a central role. The genes identified may be exploited in breeding programs to improve seed-set and yield of maize under heat stress.

Deciphering the genetic basis of root morphology, nutrient uptake, yield, and yield-related traits in rice under dry direct-seeded cultivation systems

In the face of global water scarcity, a successful transition of rice cultivation from puddled to dry direct-seeded rice (DDSR) is a future need. A genome-wide association study was performed on a complex mapping population for 39 traits: 9 seedling-establishment traits, 14 root and nutrient-uptake traits, 5 plant morphological traits, 4 lodging resistance traits, and 7 yield and yield-contributing traits. A total of 10 significant marker-trait associations (MTAs) were found along with 25 QTLs associated with 25 traits. The percent phenotypic variance explained by SNPs ranged from 8% to 84%. Grain yield was found to be significantly and positively correlated with seedling-establishment traits, root morphological traits, nutrient uptake-related traits, and grain yield-contributing traits. The genomic colocation of different root morphological traits, nutrient uptake-related traits, and grain-yield-contributing traits further supports the role of root morphological traits in improving nutrient uptake and grain yield under DDSR. The QTLs/candidate genes underlying the significant MTAs were identified. The identified promising progenies carrying these QTLs may serve as potential donors to be exploited in genomics-assisted breeding programs for improving grain yield and adaptability under DDSR.

Genome-wide association study reveals significant genomic regions for improving yield, adaptability of rice under dry direct seeded cultivation condition

BACKGROUND

Puddled transplanted system of rice cultivation despite having several benefits, is a highly labor, water and energy intensive system. In the face of changing climatic conditions, a successful transition from puddled to dry direct seeded rice (DDSR) cultivation system looks must in future. Genome-wide association study was performed for traits including, roots and nutrient uptake (14 traits), plant-morphological (5 traits), lodging-resistance (4 traits) and yield and yield attributing traits (7 traits) with the aim to identify significant marker-trait associations (MTAs) for traits enhancing rice adaptability to dry direct-seeded rice (DDSR) system.

RESULTS

Study identified a total of 37 highly significant MTAs for 20 traits. The false discovery rate (FDR) ranged from 0.264 to 3.69 × 10- 4, 0.0330 to 1.25 × 10- 4, and 0.0534 to 4.60 × 10- 6 in 2015WS, 2016DS and combined analysis, respectively. The percent phenotypic variance (PV) explained by SNPs ranged from 9 to 92%. Among the identified significant MTAs, 15 MTAs associated with the traits including nodal root, root hair length, root length density, stem and culm diameter, plant height and grain yield were reported to be located in the proximity of earlier identified candidate gene. The significant positive correlation of grain-yield with seedling establishment traits, root morphological and nutrient-uptake related traits and grain yield attributing traits pointing towards combining target traits to increase rice yield and adaptability under DDSR. Seven promising progenies with better root morphology, nutrient-uptake and higher grain yield were identified that can further be used in genomics assisted breeding for DDSR varietal development.

CONCLUSIONS

Once validated, the identified MTAs and the SNPs linked with trait of interest could be of direct use in genomic assisted breeding (GAB) to improve grain yield and adaptability of rice under DDSR.

Genome-wide association study for kernel composition and flour pasting behavior in wholemeal maize flour

BACKGROUND

Maize is a crop in high demand for food purposes and consumers worldwide are increasingly concerned with food quality. However, breeding for improved quality is a complex task and therefore developing tools to select for better quality products is of great importance. Kernel composition, flour pasting behavior, and flour particle size have been previously identified as crucial for maize-based food quality. In this work we carried out a genome-wide association study to identify genomic regions controlling compositional and pasting properties of maize wholemeal flour.

RESULTS

A collection of 132 diverse inbred lines, with a considerable representation of the food used Portuguese unique germplasm, was trialed during two seasons, and harvested samples characterized for main compositional traits, flour pasting parameters and mean particle size. The collection was genotyped with the MaizeSNP50 array. SNP-trait associations were tested using a mixed linear model accounting for genetic relatedness. Fifty-seven genomic regions were identified, associated with the 11 different quality-related traits evaluated. Regions controlling multiple traits were detected and potential candidate genes identified. As an example, for two viscosity parameters that reflect the capacity of the starch to absorb water and swell, the strongest common associated region was located near the dull endosperm 1 gene that encodes a starch synthase and is determinant on the starch endosperm structure in maize.

CONCLUSIONS

This study allowed for identifying relevant regions on the maize genome affecting maize kernel composition and flour pasting behavior, candidate genes for the majority of the quality-associated genomic regions, or the most promising target regions to develop molecular tools to increase efficacy and efficiency of quality traits selection (such as "breadability") within maize breeding programs.

Genome-Wide Association and Genomic Prediction Models of Tocochromanols in Fresh Sweet Corn Kernels

Sweet corn ( L.), a highly consumed fresh vegetable in the United States, varies for tocochromanol (tocopherol and tocotrienol) levels but makes only a limited contribution to daily intake of vitamin E and antioxidants. We performed a genome-wide association study of six tocochromanol compounds and 14 derivative traits across a sweet corn inbred line association panel to identify genes associated with natural variation for tocochromanols and vitamin E in fresh kernels. Concordant with prior studies in mature maize kernels, an association was detected between γ-tocopherol methyltransferase (vte4) and α-tocopherol content, along with () and () for tocotrienol variation. Additionally, two kernel starch synthesis genes, () and (), were associated with tocotrienols, with the strongest evidence for in combination with fixed, strong and alleles, accounting for the greater amount of tocotrienols in and lines. In prediction models with genome-wide markers, predictive abilities were higher for tocotrienols than tocopherols, and these models were superior to those that used marker sets targeting a priori genes involved in the biosynthesis and/or genetic control of tocochromanols. Through this quantitative genetic analysis, we have established a key step for increasing tocochromanols in fresh kernels of sweet corn for human health and nutrition.

Association Mapping Analysis for Fruit Quality Traits in Prunus persica Using SNP Markers

The identification of genes involved in variation of peach fruit quality would assist breeders to create new cultivars with improved fruit quality. Peach is a genetic and genomic model within the Rosaceae. A large quantity of useful data suitable for fine mapping using Single Nucleotide Polymorphisms (SNPs) from the peach genome sequence was used in this study. A set of 94 individuals from a peach germplasm collection was phenotyped and genotyped, including local Spanish and modern cultivars maintained at the Experimental Station of Aula Dei, Spain. Phenotypic evaluation based on agronomical, pomological and fruit quality traits was performed at least 3 years. A set of 4,558 out of a total of 8,144 SNPs markers developed by the Illumina Infinium BeadArray (v1.0) technology platform, covering the peach genome, were analyzed for population structure analysis and genome-wide association studies (GWAS). Population structure analysis identified two subpopulations, with admixture within them. While one subpopulation contains only modern cultivars, the other one is formed by local Spanish and several modern cultivars from international breeding programs. To test the marker trait associations between markers and phenotypic traits, four models comprising both general linear model (GLM) and mixed linear model (MLM) were selected. The MLM approach using co-ancestry values from population structure and kinship estimates (K model) identified a maximum of 347 significant associations between markers and traits. The associations found appeared to map within the interval where many candidate genes involved in different pathways are predicted in the peach genome. These results represent a promising situation for GWAS in the identification of SNP variants associated to fruit quality traits, potentially applicable in peach breeding programs.

Identification of Loci and Candidate Genes Responsible for Fiber Length in Upland Cotton (Gossypium hirsutum L.) via Association Mapping and Linkage Analyses

Fiber length (FL) is an important fiber quality trait in cotton. Although many fiber quality quantitative trait loci (QTL) responsible for FL have been identified, most cannot be applied to breeding programs, mainly due to unstable environments or large confidence intervals. In this study, we combined a genome-wide association study (GWAS) and linkage mapping to identify and validate high-quality QTLs responsible for FL. For the GWAS, we developed 93,250 high-quality single-nucleotide polymorphism (SNP) markers based on 355 accessions, and the FL was measured in eight different environments. For the linkage mapping, we constructed an F ₂ population from two extreme accessions. The high-density linkage maps spanned 3,848.29 cM, with an average marker interval of 1.41 cM. In total, 14 and 13 QTLs were identified in the association and linkage mapping analyses, respectively. Most importantly, a major QTL on chromosome D03 identified in both populations explained more than 10% of the phenotypic variation (PV). Furthermore, we found that a sucrose synthesis-related gene (Gh_D03G1338) was associated with FL in this QTL region. The RNA-seq data showed that Gh_D03G1338 was highly expressed during the fiber development stage, and the qRT-PCR analysis showed significant expression differences between the long fiber and short fiber varieties. These results suggest that Gh_D03G1338 may determine cotton fiber elongation by regulating the synthesis of sucrose. Favorable QTLs and candidate genes should be useful for increasing fiber quality in cotton breeding.

Combining Three Mapping Strategies to Reveal Quantitative Trait Loci and Candidate Genes for Maize Ear Length

Ear length (EL) is an important trait in maize ( L.) because it is positively correlated with grain yield. To understand the genetic basis of natural EL variation, a F, a four-way cross and a genome-wide association study (GWAS) population were used to identify the quantitative trait loci (QTLs) and candidate EL genes. Linkage mapping identified 14 QTLs in two types of populations from multiple environments. Six of them were located in three common genomic regions considered "stable QTLs". Candidate genes for the three stable QTLs were identified by the GWAS results. These were related to auxin transport, cell proliferation, and developmental regulation. These results confirm that maize EL is under strong genetic control by many small-effect genes. They also improve our understanding of the genetic basis of maize EL.

SSR loci potentially associated with high amylopectine content in maize kernel endosperm

As a component of functional nutrition, maize cultivars with “non-traditional” kernel composition (waxy, oilbearing, sugar, opaque, etc. phenotypic variants) are promising. Mutations in the waxy gene, which break down the structure and function of the enzyme for amylose biosynthesis, lead to a waxy (with a high content of amylopectin) endosperm formation. High variability of the waxy gene limits the use of microsatellite loci in marker associated selection of waxy maize genotypes. The increased frequency of gene rearrangements within the waxy locus facilitated the origination of many high-amylopectin corn lines carrying different SSR allelic variants. The purpose of this study was to evaluate the effectiveness of using waxy locus microsatellite sequences for identification and labeling of waxy maize genotypes. To this end, a complex of biochemical (calorimetry, bichromate method), molecular-genetic (SSR-PCR, capillary gel electrophoresis with fluorescent detection of fragments) and statistical (descriptive statistics, cluster analysis, χ2) analysis methods was used. Plant material used were 33 samples of corn kernels including mutant forms with a high content of amylose, amylopectin, short-chain starches, were kindly provided by VIR genetic collection (Russian Federation) and Maize Genetics Cooperation Stock Center (USA). The contents of starch, short-chain soluble carbohydrates, amylose, amylopectin in the grain of 33 maize samples were evaluated. Compositionally similar (to endosperm carbohydrates content) groups of samples were identified. They include 13 high-amylopectin samples carriers of waxy (wx) gene mutations and 20 samples with wild-type character (Wx). Molecular genetic screening of the collection included an analysis of the polymorphism of the microsatellite loci phi022, phi027, phi061 associated with the waxy gene sequence. Allelic composition of individual loci and their combinations were analyzed in relation to the accumulation of reserve carbohydrates in the kernel endosperm. Only the analysis of the phi022/phi027 combination or all three markers in the complex allows differentiating the wild Wx and mutant wx phenotypes of maize. It was shown that not the individual allelic polymorphisms of the phi022, phi027, phi061 loci are efficient for the markerassociated selection of high-amylopectin maize, but their unique combinations.

Joint Multi-Leaf Segmentation, Alignment, and Tracking for Fluorescence Plant Videos

This paper proposes a novel framework for fluorescence plant video processing. The plant research community is interested in the leaf-level photosynthetic analysis within a plant. A prerequisite for such analysis is to segment all leaves, estimate their structures, and track them over time. We identify this as a joint multi-leaf segmentation, alignment, and tracking problem. First, leaf segmentation and alignment are applied on the last frame of a plant video to find a number of well-aligned leaf candidates. Second, leaf tracking is applied on the remaining frames with leaf candidate transformation from the previous frame. We form two optimization problems with shared terms in their objective functions for leaf alignment and tracking respectively. A quantitative evaluation framework is formulated to evaluate the performance of our algorithm with four metrics. Two models are learned to predict the alignment accuracy and detect tracking failure respectively in order to provide guidance for subsequent plant biology analysis. The limitation of our algorithm is also studied. Experimental results show the effectiveness, efficiency, and robustness of the proposed method.

Genetic Architecture of Dietary Fiber and Oligosaccharide Content in a Middle American Panel of Edible Dry Bean

Common bean ( L.) is the most consumed edible grain legume worldwide and contains a wide range of nutrients for human health including dietary fiber. Diets high in beans are associated with lower rates of chronic diseases such as obesity and type 2 diabetes, and the content of dietary fibers varies among different market classes of dry bean. In this study, we evaluated the dietary fiber content in a Middle American diversity panel (MDP) of common bean and evaluated the genetic architecture of the various dietary fiber components. The dietary fiber components included insoluble and soluble dietary fibers as well as the antinutritional raffinose family of oligosaccharides (RFOs; raffinose, stachyose, and verbascose). All variables measured differed among market classes and entries. Colored bean seeds had higher levels of insoluble dietary fibers with the black market class showing also the highest raffinose and stachyose content. Cultivars and lines released since 1997 had higher insoluble dietary fibers and RFO content in race Durango. Higher levels of RFOs were also observed in cultivars with type II growth habit that was a recent breeding target in Durango race germplasm. Candidate genes for dietary fiber traits, especially homologs to two main genes in the RFO biosynthesis pathway, were identified. The knowledge of diversity of dietary fibers in the MDP accompanied with the identification of candidate genes could effectively improve dietary fiber components in common bean.

The first identification of genomic loci in plants associated with resistance to galling insects: a case study in Eucalyptus L'Hér. (Myrtaceae)

Genomic loci related with resistance to gall-inducing insects have not been identified in any plants. Here, association mapping was used to identify molecular markers for resistance to the gall wasp Leptocybe invasa in two Eucalyptus species. A total of 86 simple sequence repeats (SSR) markers were screened out from 839 SSRs and used for association mapping in E. grandis. By applying the mixed linear model, seven markers were identified to be associated significantly (P ≤ 0.05) with the gall wasp resistance in E. grandis, including two validated with a correction of permutation test (P ≤ 0.008). The proportion of the variance in resistance explained by a significant marker ranged from 3.3% to 37.8%. Four out of the seven significant associations in E. grandis were verified and also validated (P ≤ 0.073 in a permutation test) in E. tereticornis, with the variation explained ranging from 24.3% to 48.5%. Favourable alleles with positive effect were also mined from the significant markers in both species. These results provide insight into the genetic control of gall wasp resistance in plants and have great potential for marker-assisted selection for resistance to L. invasa in the important tree genus Eucalyptus.

The first identification of genomic loci in plants associated with resistance to galling insects: a case study in Eucalyptus L'Hér. (Myrtaceae)

Genomic loci related with resistance to gall-inducing insects have not been identified in any plants. Here, association mapping was used to identify molecular markers for resistance to the gall wasp Leptocybe invasa in two Eucalyptus species. A total of 86 simple sequence repeats (SSR) markers were screened out from 839 SSRs and used for association mapping in E. grandis. By applying the mixed linear model, seven markers were identified to be associated significantly (P ≤ 0.05) with the gall wasp resistance in E. grandis, including two validated with a correction of permutation test (P ≤ 0.008). The proportion of the variance in resistance explained by a significant marker ranged from 3.3% to 37.8%. Four out of the seven significant associations in E. grandis were verified and also validated (P ≤ 0.073 in a permutation test) in E. tereticornis, with the variation explained ranging from 24.3% to 48.5%. Favourable alleles with positive effect were also mined from the significant markers in both species. These results provide insight into the genetic control of gall wasp resistance in plants and have great potential for marker-assisted selection for resistance to L. invasa in the important tree genus Eucalyptus.

Candidate Genes for Aggressiveness in a Natural Fusarium culmorum Population Greatly Differ between Wheat and Rye Head Blight

Fusarium culmorum is one of the species causing Fusarium head blight (FHB) in cereals in Europe. We aimed to investigate the association between the nucleotide diversity of ten F. culmorum candidate genes and field ratings of aggressiveness in winter rye. A total of 100 F. culmorum isolates collected from natural infections were phenotyped for FHB at two locations and two years. Variance components for aggressiveness showed significant isolate and isolate-by-environment variance, as expected for quantitative host-pathogen interactions. Further analysis of the isolate-by-environment interaction revealed the dominant role of the isolate-by-year over isolate-by-location interaction. One single-nucleotide polymorphism (SNP) in the cutinase (CUT) gene was found to be significantly (p < 0.001) associated with aggressiveness and explained 16.05% of the genotypic variance of this trait in rye. The SNP was located 60 base pairs before the start codon, which suggests a role in transcriptional regulation. Compared to a previous study in winter wheat with the same nucleotide sequences, a larger variation of pathogen aggressiveness on rye was found and a different candidate gene was associated with pathogen aggressiveness. This is the first report on the association of field aggressiveness and a host-specific candidate gene codifying for a protein that belongs to the secretome in F. culmorum.

Genome-Wide Association Mapping of Starch Pasting Properties in Maize Using Single-Locus and Multi-Locus Models

Maize starch plays a critical role in food processing and industrial application. The pasting properties, the most important starch characteristics, have enormous influence on fabrication property, flavor characteristics, storage, cooking, and baking. Understanding the genetic basis of starch pasting properties will be beneficial for manipulation of starch properties for a given purpose. Genome-wide association studies (GWAS) are becoming a powerful tool for dissecting the complex traits. Here, we carried out GWAS for seven pasting properties of maize starch with a panel of 230 inbred lines and 145,232 SNPs using one single-locus method, genome-wide efficient mixed model association (GEMMA), and three multi-locus methods, FASTmrEMMA, FarmCPU, and LASSO. We totally identified 60 quantitative trait nucleotides (QTNs) for starch pasting properties with these four GWAS methods. FASTmrEMMA detected the most QTNs (29), followed by FarmCPU (19) and LASSO (12), GEMMA detected the least QTNs (7). Of these QTNs, seven QTNs were identified by more than one method simultaneously. We further investigated locations of these significantly associated QTNs for possible candidate genes. These candidate genes and significant QTNs provide the guidance for further understanding of molecular mechanisms of starch pasting properties. We also compared the statistical powers and Type I errors of the four GWAS methods using Monte Carlo simulations. The results suggest that the multi-locus method is more powerful than the single-locus method and a combination of these multi-locus methods could help improve the detection power of GWAS.

Association of functional markers with flowering time in lentil

In the present study, a diverse panel of 96 accessions of lentil germplasm was used to study flowering time over environments and to identify simple sequence repeat markers associated with flowering time through association mapping. The study showed high broad sense heritability estimate (h ² bs=0.93) for flowering time in lentil. Screening of 534 SSR markers resulted in an identification of 75 SSR polymorphic markers (13.9%) across studied genotypes. These markers amplified 266 loci and generated 697 alleles ranging from two to 16 alleles per locus. Model-based cluster analysis used for the determination of population structure resulted in the identification of two distinct subpopulations. Distribution of flowering time was ranged from 40 to 70 days in subpopulation I and from 54 to 69 days in subpopulation II and did not skew either late or early flowering time within a subpopulation. No admixture was observed within the subpopulations. Use of the most accepted maximum likelihood model (P3D mixed linear model with optimum compression) of MTA analysis showed significant association of 26 SSR markers with flowering time at <0.05 probability. The percent of phenotypic explained by each associated marker with flowering time ranged from 2.1 to 21.8% and identified QTLs for flowering time explaining high phenotypic variation across the environments (10.7-21.8%) or in a particular environment (10.2-21.4%). In the present study, 13 EST-SSR showed significant association with flowering time and explained large phenotypic variation (2.3-21.8%) compared to genomic SSR markers (2.1-10.2%). Hence, these markers can be used as functional markers in the lentil breeding program to develop short duration cultivars.

Linkage disequilibrium based association mapping of micronutrients in common bean (Phaseolus vulgaris L.): a collection of Jammu & Kashmir, India

Micronutrient deficiencies are of major concern in human health and plant metabolism. Iron (Fe), zinc (Zn), iodine (I), selenium (Se) are regarded as micronutrients having major impact on human health. More than 50% of populations mainly from developing countries are suffering from one or the other micronutrient malnutrition. Ensuring adequate supply of these micronutrients through diet consisting of staple foods, such as common bean (Phaseolus vulgaris L.) is must. Here, we evaluated common bean genotypes that were collected from various regions of Jammu and Kashmir, India for Fe, Zn and protein contents and used SSRs to identify the markers associated with these traits. We found significant variation among genotypes for Fe, Zn and protein contents. Genotype R2 was having 7.22 mg 100 g^-1 of Fe content, genotype K15 with 1.93 mg 100 g^-1 of Zn content and genotype KS6 with 31.6% of protein content. Diversity study was done using both cluster and structure based approach. Further, association mapping analysis using General Linear Method (GLM) approach was done to identify SSRs associated with accumulation of Fe, Zn and protein. 13 SSRs were identified that significantly (p < 0.05) showed association with Fe, Zn and protein contents in common bean. The markers associated with Fe were located on chromosome no. 2, 5, 6, 7, 9 and 10, markers associated with Zn were located on chromosome no. 1, 3, 5, 7 and 10 whereas only one marker located on chromosome no. 4 was found associated with protein content. These findings will provide potential opportunity to improve Fe and Zn concentrations in common bean, through molecular breeding.

Genome-Wide Linkage-Disequilibrium Mapping to the Candidate Gene Level in Melon (Cucumis melo)

Cucumis melo is highly diverse for fruit traits providing wide breeding and genetic research opportunities, including genome-wide association (GWA) analysis. We used a collection of 177 accessions representing the two C. melo subspecies and 11 horticultural groups for detailed characterization of fruit traits variation and evaluation of the potential of GWA for trait mapping in melon. Through genotyping-by-sequencing, 23,931 informative SNPs were selected for genome-wide analyses. We found that linkage-disequilibrium decays at ~100 Kb in this collection and that population structure effect on association results varies between traits. We mapped several monogenic traits to narrow intervals overlapping with known causative genes, demonstrating the potential of diverse collections and GWA for mapping Mendelian traits to a candidate-gene level in melon. We further report on mapping of fruit shape quantitative trait loci (QTLs) and comparison with multiple previous QTL studies. Expansion of sample size and a more balanced representation of taxonomic groups might improve efficiency for simple traits dissection. But, as in other plant species, integrated linkage-association multi-allelic approaches are likely to produce better combination of statistical power, diversity capture and mapping resolution in melon. Our data can be utilized for selection of the most appropriate accessions for such approaches.

Quantitative trait loci from identification to exploitation for crop improvement

Advancement in the field of genetics and genomics after the discovery of Mendel's laws of inheritance has led to map the genes controlling qualitative and quantitative traits in crop plant species. Mapping of genomic regions controlling the variation of quantitatively inherited traits has become routine after the advent of different types of molecular markers. Recently, the next generation sequencing methods have accelerated the research on QTL analysis. These efforts have led to the identification of more closely linked molecular markers with gene/QTLs and also identified markers even within gene/QTL controlling the trait of interest. Efforts have also been made towards cloning gene/QTLs or identification of potential candidate genes responsible for a trait. Further new concepts like crop QTLome and QTL prioritization have accelerated precise application of QTLs for genetic improvement of complex traits. In the past years, efforts have also been made in exploitation of a number of QTL for improving grain yield or other agronomic traits in various crops through markers assisted selection leading to cultivation of these improved varieties at farmers' field. In present article, we reviewed QTLs from their identification to exploitation in plant breeding programs and also reviewed that how improved cultivars developed through introgression of QTLs have improved the yield productivity in many crops.

Association mapping of starch chain length distribution and amylose content in pea (Pisum sativum L.) using carbohydrate metabolism candidate genes

BACKGROUND

Although starch consists of large macromolecules composed of glucose units linked by α-1,4-glycosidic linkages with α-1,6-glycosidic branchpoints, variation in starch structural and functional properties is found both within and between species. Interest in starch genetics is based on the importance of starch in food and industrial processes, with the potential of genetics to provide novel starches. The starch metabolic pathway is complex but has been characterized in diverse plant species, including pea.

RESULTS

To understand how allelic variation in the pea starch metabolic pathway affects starch structure and percent amylose, partial sequences of 25 candidate genes were characterized for polymorphisms using a panel of 92 diverse pea lines. Variation in the percent amylose composition of extracted seed starch and (amylopectin) chain length distribution, one measure of starch structure, were characterized for these lines. Association mapping was undertaken to identify polymorphisms associated with the variation in starch chain length distribution and percent amylose, using a mixed linear model that incorporated population structure and kinship. Associations were found for polymorphisms in seven candidate genes plus Mendel's r locus (which conditions the round versus wrinkled seed phenotype). The genes with associated polymorphisms are involved in the substrate supply, chain elongation and branching stages of the pea carbohydrate and starch metabolic pathways.

CONCLUSIONS

The association of polymorphisms in carbohydrate and starch metabolic genes with variation in amylopectin chain length distribution and percent amylose may help to guide manipulation of pea seed starch structural and functional properties through plant breeding.

Genomewide association study for seeding emergence and tiller number using SNP markers in an elite winter wheat population

Seeding emergence and tiller number are the most important traits for wheat (Triticum aestivum L.) yield, but the inheritance of seeding emergence and tillering is poorly understood. We conducted a genomewide association study focussing on seeding emergence and tiller number at different growth stages with a panel of 205 elite winter wheat accessions. The population was genotyped with a high-density Illumina iSelect 90K SNPs assay. A total of 31 loci were found to be associated with seeding emergence rate (SER) and tiller number in different growth stages. Loci distributed among 12 chromosomes accounted for 5.35 to 11.33% of the observed phenotypic variation. With this information, 10 stable SNPs were identified for eventual development of cleaved amplified polymorphic sequence markers for SER and tiller number in different growth stages. Additionally, a set of elite alleles were identified, such as Ra_c14761_1348-T, which may increase SER by 13.35%, and Excalibur_c11045_236-A and BobWhite_c8436_391-T, which may increase the rate of available tillering by 14.78 and 8.47%, respectively. These results should provide valuable information for marker-assisted selection and parental selection in wheat breeding programmes.

Genetic Analysis of Teosinte Alleles for Kernel Composition Traits in Maize

Teosinte (Zea mays ssp. parviglumis) is the wild ancestor of modern maize (Zea mays ssp. mays). Teosinte contains greater genetic diversity compared with maize inbreds and landraces, but its use is limited by insufficient genetic resources to evaluate its value. A population of teosinte near isogenic lines (NILs) was previously developed to broaden the resources for genetic diversity of maize, and to discover novel alleles for agronomic and domestication traits. The 961 teosinte NILs were developed by backcrossing 10 geographically diverse parviglumis accessions into the B73 (reference genome inbred) background. The NILs were grown in two replications in 2009 and 2010 in Columbia, MO and Aurora, NY, respectively, and near infrared reflectance spectroscopy and nuclear magnetic resonance calibrations were developed and used to rapidly predict total kernel starch, protein, and oil content on a dry matter basis in bulk whole grains of teosinte NILs. Our joint-linkage quantitative trait locus (QTL) mapping analysis identified two starch, three protein, and six oil QTL, which collectively explained 18, 23, and 45% of the total variation, respectively. A range of strong additive allelic effects for kernel starch, protein, and oil content were identified relative to the B73 allele. Our results support our hypothesis that teosinte harbors stronger alleles for kernel composition traits than maize, and that teosinte can be exploited for the improvement of kernel composition traits in modern maize germplasm.

Genetic dissection of sorghum grain quality traits using diverse and segregating populations

KEY MESSAGE

Coordinated association and linkage mapping identified 25 grain quality QTLs in multiple environments, and fine mapping of the Wx locus supports the use of high-density genetic markers in linkage mapping. There is a wide range of end-use products made from cereal grains, and these products often demand different grain characteristics. Fortunately, cereal crop species including sorghum [Sorghum bicolor (L.) Moench] contain high phenotypic variation for traits influencing grain quality. Identifying genetic variants underlying this phenotypic variation allows plant breeders to develop genotypes with grain attributes optimized for their intended usage. Multiple sorghum mapping populations were rigorously phenotyped across two environments (SC Coastal Plain and Central TX) in 2 years for five major grain quality traits: amylose, starch, crude protein, crude fat, and gross energy. Coordinated association and linkage mapping revealed several robust QTLs that make prime targets to improve grain quality for food, feed, and fuel products. Although the amylose QTL interval spanned many megabases, the marker with greatest significance was located just 12 kb from waxy (Wx), the primary gene regulating amylose production in cereal grains. This suggests higher resolution mapping in recombinant inbred line (RIL) populations can be obtained when genotyped at a high marker density. The major QTL for crude fat content, identified in both a RIL population and grain sorghum diversity panel, encompassed the DGAT1 locus, a critical gene involved in maize lipid biosynthesis. Another QTL on chromosome 1 was consistently mapped in both RIL populations for multiple grain quality traits including starch, crude protein, and gross energy. Collectively, these genetic regions offer excellent opportunities to manipulate grain composition and set up future studies for gene validation.

Identification of QTL for maize grain yield and kernel-related traits

Grain yield (GY) is one of the most important and complex quantitative traits in maize (Zea mays L.) breeding practice. Quantitative trait loci (QTLs) for GY and three kernel-related traits were detected in a set of recombinant inbred lines (RILs). One hundred and seven simple sequence repeats (SSRs) and 168 insertion/deletion polymorphism markers (Indels) were used to genotype RILs. Eight QTLs were found to be associated with four yield-related traits: GY, 100-kernel weight (HKW), 10-kernel length (KL), and 10-kernel length width (KW). Each QTL explained between 5.96 (qKL2-1) and 13.05 (qKL1-1) per cent of the phenotypic variance. Notably, one common QTL, located at the marker interval between bnlg1893 and chr2- 236477 (chromosomal bin 2.09) simultaneously controlled GY and HKW; another common QTL, at bin 2.03 was simultaneously responsible for HKW and KW. Of the QTLs identified, only one pair of significant epistatic interaction involved in chromosomal region at bin 2.03 was detected for HKW; no significant QTL × environment interactions were observed. These results provide the common QTLs and for marker-assisted breeding.

Genetic architecture of kernel composition in global sorghum germplasm

Background

Sorghum [Sorghum bicolor (L.) Moench] is an important cereal crop for dryland areas in the United States and for small-holder farmers in Africa. Natural variation of sorghum grain composition (protein, fat, and starch) between accessions can be used for crop improvement, but the genetic controls are still unresolved. The goals of this study were to quantify natural variation of sorghum grain composition and to identify single-nucleotide polymorphisms (SNPs) associated with variation in grain composition concentrations.

Results

In this study, we quantified protein, fat, and starch in a global sorghum diversity panel using near-infrared spectroscopy (NIRS). Protein content ranged from 8.1 to 18.8%, fat content ranged from 1.0 to 4.3%, and starch content ranged from 61.7 to 71.1%. Durra and bicolor-durra sorghum from Ethiopia and India had the highest protein and fat and the lowest starch content, while kafir sorghum from USA, India, and South Africa had the lowest protein and the highest starch content. Genome-wide association studies (GWAS) identified quantitative trait loci (QTL) for sorghum protein, fat, and starch. Previously published RNAseq data was used to identify candidate genes within a GWAS QTL region. A putative alpha-amylase 3 gene, which has previously been shown to be associated with grain composition traits, was identified as a strong candidate for protein and fat variation.

Conclusions

We identified promising sources of genetic material for manipulation of grain composition traits, and several loci and candidate genes that may control sorghum grain composition. This survey of grain composition in sorghum germplasm and identification of protein, fat, and starch QTL contributes to our understanding of the genetic basis of natural variation in sorghum grain nutritional traits.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3403-x) contains supplementary material, which is available to authorized users.

Genome-Wide Association Study in Wheat Identifies Resistance to the Cereal Cyst Nematode Heterodera filipjevi

The cyst nematode Heterodera filipjevi is a plant parasite causing substantial yield loss in wheat. Resistant cultivars are the preferred method of controlling cyst nematodes. Association mapping is a powerful approach to detect associations between phenotypic variation and genetic polymorphisms; in this way favorable traits such as resistance to pathogens can be located. Therefore, a genome-wide association study of 161 winter wheat accessions was performed with a 90K iSelect single nucleotide polymorphism (SNP) chip. Population structure analysis grouped into two major subgroups and first principal component accounted 6.16% for phenotypic diversity. The genome-wide linkage disequilibrium across wheat was 3 cM. Eleven quantitative trait loci (QTLs) on chromosomes 1AL, 2AS, 2BL, 3AL, 3BL, 4AS, 4AL, 5BL, and 7BL were identified using a mixed linear model false discovery rate of P < 0.01 that explained 43% of total genetic variation. This is the first report of QTLs conferring resistance to H. filipjevi in wheat. Eight QTLs on chromosomes 1AL, 2AS, 2BL, 3AL, 4AL, and 5BL were linked to putative genes known to be involved in plant-pathogen interactions. Two other QTLs on 3BL and one QTL on 7BL linked to putative genes known to be involved in abiotic stress.

Genome wide association mapping for grain shape traits in indica rice

Using genome-wide association mapping, 47 SNPs within 27 significant loci were identified for four grain shape traits, and 424 candidate genes were predicted from public database. Grain shape is a key determinant of grain yield and quality in rice (Oryza sativa L.). However, our knowledge of genes controlling rice grain shape remains limited. Genome-wide association mapping based on linkage disequilibrium (LD) has recently emerged as an effective approach for identifying genes or quantitative trait loci (QTL) underlying complex traits in plants. In this study, association mapping based on 5291 single nucleotide polymorphisms (SNPs) was conducted to identify significant loci associated with grain shape traits in a global collection of 469 diverse rice accessions. A total of 47 SNPs were located in 27 significant loci for four grain traits, and explained ~44.93-65.90 % of the phenotypic variation for each trait. In total, 424 candidate genes within a 200 kb extension region (±100 kb of each locus) of these loci were predicted. Of them, the cloned genes GS3 and qSW5 showed very strong effects on grain length and grain width in our study. Comparing with previously reported QTLs for grain shape traits, we found 11 novel loci, including 3, 3, 2 and 3 loci for grain length, grain width, grain length-width ratio and thousand grain weight, respectively. Validation of these new loci would be performed in the future studies. These results revealed that besides GS3 and qSW5, multiple novel loci and mechanisms were involved in determining rice grain shape. These findings provided valuable information for understanding of the genetic control of grain shape and molecular marker assistant selection (MAS) breeding in rice.

A Genome-Wide Association Study for Partial Resistance to Maize Common Rust

Quantitative resistance to maize common rust (causal agent Puccinia sorghi) was assessed in an association mapping population of 274 diverse inbred lines. Resistance to common rust was found to be moderately correlated with resistance to three other diseases and with the severity of the hypersensitive defense response previously assessed in the same population. Using a mixed linear model accounting for the confounding effects of population structure and flowering time, genome-wide association tests were performed based at 246,497 single-nucleotide polymorphism loci. Three loci associated with maize common rust resistance were identified. Candidate genes at each locus had predicted roles, mainly in cell wall modification. Other candidate genes included a resistance gene and a gene with a predicted role in regulating accumulation of reactive oxygen species.

Identification and reproducibility of diagnostic DNA markers for tuber starch and yield optimization in a novel association mapping population of potato (Solanum tuberosum L.)

SNPs in candidate genes Pain - 1, InvCD141 (invertases), SSIV (starch synthase), StCDF1 (transcription factor), LapN (leucine aminopeptidase), and cytoplasm type are associated with potato tuber yield, starch content and/or starch yield. Tuber yield (TY), starch content (TSC), and starch yield (TSY) are complex characters of high importance for the potato crop in general and for industrial starch production in particular. DNA markers associated with superior alleles of genes that control the natural variation of TY, TSC, and TSY could increase precision and speed of breeding new cultivars optimized for potato starch production. Diagnostic DNA markers are identified by association mapping in populations of tetraploid potato varieties and advanced breeding clones. A novel association mapping population of 282 genotypes including varieties, breeding clones and Andean landraces was assembled and field evaluated in Northern Spain for TY, TSC, TSY, tuber number (TN) and tuber weight (TW). The landraces had lower mean values of TY, TW, TN, and TSY. The population was genotyped for 183 microsatellite alleles, 221 single nucleotide polymorphisms (SNPs) in fourteen candidate genes and eight known diagnostic markers for TSC and TSY. Association test statistics including kinship and population structure reproduced five known marker-trait associations of candidate genes and discovered new ones, particularly for tuber yield and starch yield. The inclusion of landraces increased the number of detected marker-trait associations. Integration of the present association mapping results with previous QTL linkage mapping studies for TY, TSC, TSY, TW, TN, and tuberization revealed some hot spots of QTL for these traits in the potato genome. The genomic positions of markers linked or associated with QTL for complex tuber traits suggest high multiplicity and genome wide distribution of the underlying genes.

Evolution of DUF1313 family members across plant species and their association with maize photoperiod sensitivity

Proteins of the DUF1313 family contain a highly conserved domain and are only found in plants; they play important roles in most plant functions. In this study, 269 DUF1313 genes from 81 photoautotrophic species were identified; they were classified into three major types based on the amino acid substitutions in the conserved region: IARV, I(S/T/F)(K/R)V, and IRRV. Phylogenic tree constructed from 51 DUF1313 genes from graminoids revealed three clades: A, B1, and B2. Clade B1 was found to have undergone episodic positive selection after a gene duplication event and included four amino acid sites under positive selection. The association between DUF1313 family members and traits investigated in maize indicated that three of four genes (GRMZM2G025646, GRMZM5G877647, GRMZM2G359322, and GRMZM2G382774) were associated with the target traits such as days to silking, days to tasselling, and plant height. The nucleotide diversity of the most primitive and highly conserved DUF1313 gene, ELF4-like4, was the highest in Tripsacum and the lowest in maize. Tajima's D and Fu and Li's D tests revealed that significant purifying selection had occurred in the coding sequence region of this DUF1313 gene in teosinte and maize. No significant signal was detected in the 5'-untranslated region of this gene in each of the three species (maize, teosinte, and Tripsacum) or in any gene regions of Tripsacum. Phylogenetic analyses revealed that the 103 accessions of maize, teosinte, and Tripsacum can be grouped into four clades based on the ELF4-like4 gene sequence similarity. Thus, this gene can be used to determine the relationships between maize and its relatives, and the DUF1313 family members and alleles identified in this study might be valuable genetic resources for molecular marker-assisted breeding in maize.

Combined Linkage and Association Mapping Reveals QTL and Candidate Genes for Plant and Ear Height in Maize

Plant height (PH) and ear height (EH) are two very important agronomic traits related to the population density and lodging in maize. In order to better understand of the genetic basis of nature variation in PH and EH, two bi-parental populations and one genome-wide association study (GWAS) population were used to map quantitative trait loci (QTL) for both traits. Phenotypic data analysis revealed a wide normal distribution and high heritability for PH and EH in the three populations, which indicated that maize height is a highly polygenic trait. A total of 21 QTL for PH and EH in three common genomic regions (bin 1.05, 5.04/05, and 6.04/05) were identified by QTL mapping in the two bi-parental populations under multiple environments. Additionally, 41 single nucleotide polymorphisms (SNPs) were identified for PH and EH by GWAS, of which 29 SNPs were located in 19 unique candidate gene regions. Most of the candidate genes were related to plant growth and development. One QTL on Chromosome 1 was further verified in a near-isogenic line (NIL) population, and GWAS identified a C2H2 zinc finger family protein that maybe the candidate gene for this QTL. These results revealed that nature variation of PH and EH are strongly controlled by multiple genes with low effect and facilitated a better understanding of the underlying mechanism of height in maize.

Genetic basis of maize kernel starch content revealed by high-density single nucleotide polymorphism markers in a recombinant inbred line population

BACKGROUND

Starch from maize kernels has diverse applications in human and animal diets and in industry and manufacturing. To meet the demands of these applications, starch quantity and quality need improvement, which requires a clear understanding of the functional mechanisms involved in starch biosynthesis and accumulation. In this study, a recombinant inbred line (RIL) population was developed from a cross between inbred lines CI7 and K22. The RIL population, along with both parents, was grown in three environments, and then genotyped using the MaizeSNP50 BeadChip and phenotyped to dissect the genetic architecture of starch content in maize kernels.

RESULTS

Based on the genetic linkage map constructed using 2,386 bins as markers, six quantitative trait loci (QTLs) for starch content in maize kernels were detected in the CI7/K22 RIL population. Each QTL accounted for 4.7% (qSTA9-1) to 10.6% (qSTA4-1) of the starch variation. The QTL interval was further reduced using the bin-map method, with the physical distance of a single bin at the QTL peak ranging from 81.7 kb to 2.2 Mb. Based on the functional annotations and prior knowledge of the genes in the top bin, seven genes were considered as potential candidate genes for the identified QTLs. Three of the genes encode enzymes in non-starch metabolism but may indirectly affect starch biosynthesis, and four genes may act as regulators of starch biosynthesis.

CONCLUSIONS

A few large-effect QTLs, together with a certain number of minor-effect QTLs, mainly contribute to the genetic architecture of kernel starch content in our maize biparental linkage population. All of the identified QTLs, especially the large-effect QTL, qSTA4-1, with a small QTL interval, will be useful for improving the maize kernel starch content through molecular breeding.

Using genome-wide associations to identify metabolic pathways involved in maize aflatoxin accumulation resistance

BACKGROUND

Aflatoxin is a potent carcinogen that can contaminate grain infected with the fungus Aspergillus flavus. However, resistance to aflatoxin accumulation in maize is a complex trait with low heritability. Here, two complementary analyses were performed to better understand the mechanisms involved. The first coupled results of a genome-wide association study (GWAS) that accounted for linkage disequilibrium among single nucleotide polymorphisms (SNPs) with gene-set enrichment for a pathway-based approach. The rationale was that the cumulative effects of genes in a pathway would give insight into genetic differences that distinguish resistant from susceptible lines of maize. The second involved finding non-pathway genes close to the most significant SNP-trait associations with the greatest effect on reducing aflatoxin in multiple environments. Unlike conventional GWAS, the latter analysis emphasized multiple aspects of SNP-trait associations rather than just significance and was performed because of the high genotype x environment variability exhibited by this trait.

RESULTS

The most significant metabolic pathway identified was jasmonic acid (JA) biosynthesis. Specifically, there was at least one allelic variant for each step in the JA biosynthesis pathway that conferred an incremental decrease to the level of aflatoxin observed among the inbred lines in the GWAS panel. Several non-pathway genes were also consistently associated with lowered aflatoxin levels. Those with predicted functions related to defense were: leucine-rich repeat protein kinase, expansin B3, reversion-to-ethylene sensitivity1, adaptor protein complex2, and a multidrug and toxic compound extrusion protein.

CONCLUSIONS

Our genetic analysis provided strong evidence for several genes that were associated with aflatoxin resistance. Inbred lines that exhibited lower levels of aflatoxin accumulation tended to share similar haplotypes for genes specifically in the pathway of JA biosynthesis, along with several non-pathway genes with putative defense-related functions. Knowledge gained from these two complementary analyses has improved our understanding of population differences in aflatoxin resistance.

Tracking sesamin synthase gene expression through seed maturity in wild and cultivated sesame species--a domestication footprint

Sesamin and sesamolin are the major oil-soluble lignans present in sesame seed, having a wide range of biological functions beneficial to human health. Understanding sesame domestication history using sesamin synthase gene expression could enable delineation of the sesame putative progenitor. This report examined the functional expression of sesamin synthase (CYP81Q1) during capsule maturation (0-40 days after flowering) in three wild Sesamum species and four sesame cultivars. Among the cultivated accessions, only S. indicum (CO-1) exhibited transcript abundance of sesamin synthase along with high sesamin content similar to S. malabaricum, while the other cultivated sesame showed low expression. The sesamin synthase expression analysis, coupled with quantification of sesamin level, indicates that sesamin synthase was not positively favoured during domestication. The sesamin synthase expression pattern and lignan content, along with phylogenetic analysis suggested a close relationship of cultivated sesame and the wild species S. malabaricum. The high genetic identity between the two species S. indicum and S. malabaricum points towards the role of the putative progenitor S. malabaricum in sesame breeding programmes to broaden the genetic base of sesame cultivars. This study emphasises the need to investigate intraspecific and interspecific variation in the primary, secondary and tertiary gene pools to develop superior sesame genotypes.

Genetic Determinants of the Network of Primary Metabolism and Their Relationships to Plant Performance in a Maize Recombinant Inbred Line Population

Deciphering the influence of genetics on primary metabolism in plants will provide insights useful for genetic improvement and enhance our fundamental understanding of plant growth and development. Although maize (Zea mays) is a major crop for food and feed worldwide, the genetic architecture of its primary metabolism is largely unknown. Here, we use high-density linkage mapping to dissect large-scale metabolic traits measured in three different tissues (leaf at seedling stage, leaf at reproductive stage, and kernel at 15 d after pollination [DAP]) of a maize recombinant inbred line population. We identify 297 quantitative trait loci (QTLs) with moderate (86.2% of the mapped QTL, R(2) = 2.4 to 15%) to major effects (13.8% of the mapped QTL, R(2) >15%) for 79 primary metabolites across three tissues. Pairwise epistatic interactions between these identified loci are detected for more than 25.9% metabolites explaining 6.6% of the phenotypic variance on average (ranging between 1.7 and 16.6%), which implies that epistasis may play an important role for some metabolites. Key candidate genes are highlighted and mapped to carbohydrate metabolism, the tricarboxylic acid cycle, and several important amino acid biosynthetic and catabolic pathways, with two of them being further validated using candidate gene association and expression profiling analysis. Our results reveal a metabolite-metabolite-agronomic trait network that, together with the genetic determinants of maize primary metabolism identified herein, promotes efficient utilization of metabolites in maize improvement.

Identification of Genetic Loci Associated with Quality Traits in Almond via Association Mapping

To design an appropriate association study, we need to understand population structure and the structure of linkage disequilibrium within and among populations as well as in different regions of the genome in an organism. In this study, we have used a total of 98 almond accessions, from five continents located and maintained at the Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA; Spain), and 40 microsatellite markers. Population structure analysis performed in 'Structure' grouped the accessions into two principal groups; the Mediterranean (Western-Europe) and the non-Mediterranean, with K = 3, being the best fit for our data. There was a strong subpopulation structure with linkage disequilibrium decaying with increasing genetic distance resulting in lower levels of linkage disequilibrium between more distant markers. A significant impact of population structure on linkage disequilibrium in the almond cultivar groups was observed. The mean r2 value for all intra-chromosomal loci pairs was 0.040, whereas, the r2 for the inter-chromosomal loci pairs was 0.036. For analysis of association between the markers and phenotypic traits, five models comprising both general linear models and mixed linear models were selected to test the marker trait associations. The mixed linear model (MLM) approach using co-ancestry values from population structure and kinship estimates (K model) as covariates identified a maximum of 16 significant associations for chemical traits and 12 for physical traits. This study reports for the first time the use of association mapping for determining marker-locus trait associations in a world-wide almond germplasm collection. It is likely that association mapping will have the most immediate and largest impact on the tier of crops such as almond with the greatest economic value.

A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes

BACKGROUND

Cassava, Manihot esculenta Crantz, is one of the most important crops world-wide representing the staple security for more than one billion of people. The development of dense genetic and physical maps, as the basis for implementing genetic and molecular approaches to accelerate the rate of genetic gains in breeding program represents a significant challenge. A reference genome sequence for cassava has been made recently available and community efforts are underway for improving its quality. Cassava is threatened by several pathogens, but the mechanisms of defense are far from being understood. Besides, there has been a lack of information about the number of genes related to immunity as well as their distribution and genomic organization in the cassava genome.

RESULTS

A high dense genetic map of cassava containing 2,141 SNPs has been constructed. Eighteen linkage groups were resolved with an overall size of 2,571 cM and an average distance of 1.26 cM between markers. More than half of mapped SNPs (57.4%) are located in coding sequences. Physical mapping of scaffolds of cassava whole genome sequence draft using the mapped markers as anchors resulted in the orientation of 687 scaffolds covering 45.6% of the genome. One hundred eighty nine new scaffolds are anchored to the genetic cassava map leading to an extension of the present cassava physical map with 30.7 Mb. Comparative analysis using anchor markers showed strong co-linearity to previously reported cassava genetic and physical maps. In silico based searching for conserved domains allowed the annotation of a repertory of 1,061 cassava genes coding for immunity-related proteins (IRPs). Based on physical map of the corresponding sequencing scaffolds, unambiguous genetic localization was possible for 569 IRPs.

CONCLUSIONS

This is the first study reported so far of an integrated high density genetic map using SNPs with integrated genetic and physical localization of newly annotated immunity related genes in cassava. These data build a solid basis for future studies to map and associate markers with single loci or quantitative trait loci for agronomical important traits. The enrichment of the physical map with novel scaffolds is in line with the efforts of the cassava genome sequencing consortium.

Genome wide association study for drought, aflatoxin resistance, and important agronomic traits of maize hybrids in the sub-tropics

The primary maize (Zea mays L.) production areas are in temperate regions throughout the world and this is where most maize breeding is focused. Important but lower yielding maize growing regions such as the sub-tropics experience unique challenges, the greatest of which are drought stress and aflatoxin contamination. Here we used a diversity panel consisting of 346 maize inbred lines originating in temperate, sub-tropical and tropical areas testcrossed to stiff-stalk line Tx714 to investigate these traits. Testcross hybrids were evaluated under irrigated and non-irrigated trials for yield, plant height, ear height, days to anthesis, days to silking and other agronomic traits. Irrigated trials were also inoculated with Aspergillus flavus and evaluated for aflatoxin content. Diverse maize testcrosses out-yielded commercial checks in most trials, which indicated the potential for genetic diversity to improve sub-tropical breeding programs. To identify genomic regions associated with yield, aflatoxin resistance and other important agronomic traits, a genome wide association analysis was performed. Using 60,000 SNPs, this study found 10 quantitative trait variants for grain yield, plant and ear height, and flowering time after stringent multiple test corrections, and after fitting different models. Three of these variants explained 5-10% of the variation in grain yield under both water conditions. Multiple identified SNPs co-localized with previously reported QTL, which narrows the possible location of causal polymorphisms. Novel significant SNPs were also identified. This study demonstrated the potential to use genome wide association studies to identify major variants of quantitative and complex traits such as yield under drought that are still segregating between elite inbred lines.