The MaizeGDB Genome Browser tutorial: one example of database outreach to biologists via video

Genome-Wide Association Study and Genomic Predictions for Hydroxycinnamate Concentrations in Maize Stover

Hydroxycinnamates, like ferulate (FA) and p-coumarate (pCA), are important components of maize cell walls, which influence pest resistance, ruminal digestibility, and biofuel production. Increasing their concentration has been linked to increased pest resistance, but also may lead to a decrease in nutritional value or bioethanol production efficiency. Therefore, improving forage quality or biofuel production without compromising plant resistance and a thorough understanding of the biosynthesis and deposition of these compounds is necessary, especially in stover, which is the feedstock for second-generation biofuel production and determines animal forage quality. This study aimed to identify genomic regions associated with hydroxycinnamates and to develop genomic prediction models to determine the best selection approach to modify hydroxycinnamate content. Although heritability estimates for hydroxycinnamates were moderate, direct phenotypic selection is discouraged because hydroxycinnamate quantification is laborious and time-consuming. Negative genotypic correlations were observed between animal digestibility and pCA content and positive with diferulates content, suggesting differing effects compared to previous studies on maize pith. However, no colocalizations with digestibility QTLs were found, highlighting the need for further research. Given the moderate predictive capacity of GBLUP prediction models, genotypic selection is proposed as the most promising alternative for modifying hydroxycinnamate content.

Screening and Validation of Leaf Width-Related Genes in Inbred Maize Lines

Leaf width is a key determinant of planting density and photosynthetic efficiency. In an effort to determine which genes regulate maize plant leaf width, we performed a genome-wide association study (GWAS) of 1.49 × 106 single nucleotide polymorphisms (SNPs) in 80 sequenced backbone inbred maize lines in Jilin Province, China, based upon phenotypic leaf width data from two years. In total, 14 SNPs were identified as being significantly related to leaf width (p < 0.000001), with these SNPs being located on chromosomes 1, 2, 3, 5, 6, 7, 8, and 9. A total of five candidate genes were identified within a mean linkage disequilibrium (LD) distance of 9.7 kb, with a significant SNP being identified within the Zm00001d044327 candidate gene. RNA was then isolated from 12 different inbred maize lines from this GWAS study cohort and was used to conduct qPCR analyses which revealed significant differences in Zm00001d044327 expression among strains exhibiting significant differences in leaf width. Based on an assessment of EMS mutant lines harboring a conserved amino acid stop mutation and two non-synonymous mutations in Zm00001d044327 that exhibited a narrow leaf width, these data suggested that Zm00001d044327 is a key regulator of maize leaf width.

Genomics of maize resistance to kernel contamination with fumonisins using a multiparental advanced generation InterCross maize population (MAGIC)

Maize kernel is exposed to several fungal species, most notably Fusarium verticillioides, which can contaminate maize kernels with fumonisins. In an effort to increase genetic gains and avoid the laborious tasks of conventional breeding, the use of marker-assisted selection or genomic selection programs was proposed. To this end, in the present study a Genome Wide Association Study (GWAS) was performed on 339 RILs of a Multiparental Advanced Generation InterCross (MAGIC) population that had previously been used to locate Quantitative Trait Locus (QTL) for resistance to Fusarium Ear Rot (FER). Six QTLs for fumonisin content were detected in the bins 3.08, 4.07, 4.10, 7.03-7.04, 9.04-9.05 and 10.04-10.5. Five of the six QTLs collocate in regions where QTLs for FER were also found. However, the genetic variation for fumonisin content in kernel is conditioned by many other QTLs of small effect that could show QTL x environment interaction effects. Although a genomic selection approach to directly reduce fumonisin content in the kernel could be suitable, improving resistance to fumonisin content by genomic selection for FER would be more advisable.

Precision Mapping of a Maize MAGIC Population Identified a Candidate Gene for the Senescence-Associated Physiological Traits

Senescence is an important trait in maize (Zea mais L.), a key crop that provides nutrition values and a renewable source of bioenergy worldwide. Genome-wide association studies (GWAS) can be used to identify causative genetic variants that influence the major physiological measures of senescence, which is used by plants as a defense mechanism against abiotic and biotic stresses affecting its performance. We measured four physiological and two agronomic traits that affect senescence. Six hundred seventy-two recombinant inbred lines (RILs) were evaluated in two consecutive years. Thirty-six candidate genes were identified by genome-wide association study (GWAS), and 11 of them were supported by additional evidence for involvement in senescence-related processes including proteolysis, sugar transport, and sink activity. We identified a candidate gene, Zm00001d043586, significantly associated with chlorophyll, and independently studied its transcription expression in an independent panel. Our results showed that Zm00001d043586 affects chlorophyl rate degradation, a key determinant of senescence, at late plant development stages. These results contribute to better understand the genetic relationship of the important trait senescence with physiology related parameters in maize and provide new putative molecular markers that can be used in marker assisted selection for line development.

Plant homeodomain proteins provide a mechanism for how leaves grow wide

The mechanisms whereby leaf anlagen undergo proliferative growth and expansion to form wide, flat leaves are unclear. The maize gene NARROWSHEATH1 (NS1) is a WUSCHEL-related homeobox3 (WOX3) homolog expressed at the margins of leaf primordia, and is required for mediolateral outgrowth. To investigate the mechanisms of NS1 function, we used chromatin immunoprecipitation and laser-microdissection RNA-seq of leaf primordial margins to identify gene targets bound and modulated by NS1. Microscopic analyses of cell division and gene expression in expanding leaves, and reverse genetic analyses of homologous NS1 target genes in Arabidopsis, reveal that NS1 controls mediolateral outgrowth by repression of a growth inhibitor and promotion of cell division at primordial leaf margins. Intriguingly, homologous WOX gene products are expressed in stem cell-organizing centers and traffic to adjoining cells to activate stem-cell identity non-autonomously. In contrast, WOX3/NS1 does not traffic, and stimulates cell divisions in the same cells in which it is transcribed.

Highlighted Article: The NS1 homeodomain transcription factor regulates lateral organ outgrowth from shoot meristems and leaf primordial margins by repressing the expression of negative growth regulators.

Genome-wide association analysis for fumonisin content in maize kernels

BACKGROUND

Plant breeding has been proposed as one of the most effective and environmentally safe methods to control fungal infection and to reduce fumonisin accumulation. However, conventional breeding can be hampered by the complex genetic architecture of resistance to fumonisin accumulation and marker-assisted selection is proposed as an efficient alternative. In the current study, GWAS has been performed for the first time for detecting high-resolution QTL for resistance to fumonisin accumulation in maize kernels complementing published GWAS results for Fusarium ear rot.

RESULTS

Thirty-nine SNPs significantly associated with resistance to fumonisin accumulation in maize kernels were found and clustered into 17 QTL. Novel QTLs for fumonisin content would be at bins 3.02, 5.02, 7.05 and 8.07. Genes with annotated functions probably implicated in resistance to pathogens based on previous studies have been highlighted.

CONCLUSIONS

Breeding approaches to fix favorable functional variants for genes implicated in maize immune response signaling may be especially useful to reduce kernel contamination with fumonisins without significantly interfering in mycelia development and growth and, consequently, in the beneficial endophytic behavior of Fusarium verticillioides.

Genome-wide haplotype-based association analysis of key traits of plant lodging and architecture of maize identifies major determinants for leaf angle: hapLA4

Traits related to plant lodging and architecture are important determinants of plant productivity in intensive maize cultivation systems. Motivated by the identification of genomic associations with the leaf angle, plant height (PH), ear height (EH) and the EH/PH ratio, we characterized approximately 7,800 haplotypes from a set of high-quality single nucleotide polymorphisms (SNPs), in an association panel consisting of tropical maize inbred lines. The proportion of the phenotypic variations explained by the individual SNPs varied between 7%, for the SNP S1_285330124 (located on chromosome 9 and associated with the EH/PH ratio), and 22%, for the SNP S1_317085830 (located on chromosome 6 and associated with the leaf angle). A total of 40 haplotype blocks were significantly associated with the traits of interest, explaining up to 29% of the phenotypic variation for the leaf angle, corresponding to the haplotype hapLA4.04, which was stable over two growing seasons. Overall, the associations for PH, EH and the EH/PH ratio were environment-specific, which was confirmed by performing a model comparison analysis using the information criteria of Akaike and Schwarz. In addition, five stable haplotypes (83%) and 15 SNPs (75%) were identified for the leaf angle. Finally, approximately 62% of the associated haplotypes (25/40) did not contain SNPs detected in the association study using individual SNP markers. This result confirms the advantage of haplotype-based genome-wide association studies for examining genomic regions that control the determining traits for architecture and lodging in maize plants.

Screening and verification of genes associated with leaf angle and leaf orientation value in inbred maize lines

Leaf angle and leaf orientation value are important traits affecting planting density and photosynthetic efficiency. To identify the genes involved in controlling leaf angle and leaf orientation value, we utilized 1.49×10(6) single nucleotide polymorphism (SNP) markers obtained after sequencing 80 backbone inbred maize lines in Jilin Province, based on phenotype data from two years, and analyzed these two traits in a genome-wide association study (GWAS). A total of 33 SNPs were significantly associated (P<0.000001) with the two target traits. Twenty-two SNPs were significantly associated with leaf angle and distributed on chromosomes 1, 3, 4, 5, 6, 7, 8, and 9, explaining 21.62% of the phenotypic variation. Eleven SNPs were significantly associated with leaf orientation value and distributed on chromosomes 1, 3, 4, 5, 6, 7, and 9, explaining 29.63% of the phenotypic variation. Within the mean linkage disequilibrium (LD) distance of 9.7 kb for the significant SNP locus, 22 leaf angle candidate genes were detected, and 3 of these candidate genes harbored significant SNPs, with phenotype contribution rates greater than 10%. Two candidate genes at distances less than 100 bp from significant SNPs showed phenotype contribution rates greater than 8%. Seven leaf orientation value candidate genes were detected: 3 of these candidate genes harbored significant SNPs, with phenotype contribution rates greater than 10%. Eight inbred maize lines with significant differences in leaf angle and leaf orientation value were selected to test candidate gene expression levels from 182 recombinant inbred lines (RILs). The 5 leaf angle candidate genes and 3 leaf orientation value candidate genes were verified using quantitative real-time PCR (qRT-PCR). The results showed significant differences in the expression levels of the above eight genes between inbred maize lines with significant differences in leaf angle and leaf orientation value.

Genome wide association study for gray leaf spot resistance in tropical maize core

Gray leaf spot is a maize foliar disease with worldwide distribution and can drastically reduce the production in susceptible genotypes. Published works indicate that resistance to gray leaf spot is a complex trait controlled by multiple genes, with additive effect and influenced by environment. The aim of this study was to identify genomic regions, including putative genes, associated with resistance to gray leaf spot under natural conditions of disease occurrence. A genome wide association study was conducted with 355,972 single nucleotide polymorphism markers on a phenotypic data composed by 157 tropical maize inbred lines, evaluated at Maringá -Brazil. Seven single nucleotide polymorphisms were significantly associated with gray leaf spot, some of which were localized to previously reported quantitative trait loci regions. Three gene models linked to the associated single nucleotide polymorphism were expressed at flowering time and tissue related with gray leaf spot infection, explaining a considerable proportion of the phenotypic variance, ranging from 0.34 to 0.38. The gene model GRMZM2G073465 (bin 10.07) encodes a cysteine protease3 protein, gene model GRMZM2G007188 (bin 1.02) expresses a rybosylation factor-like protein and the gene model GRMZM2G476902 (bin 4.08) encodes an armadillo repeat protein. These three proteins are related with plant defense pathway. Once these genes are validated in next studies, they will be useful for marker-assisted selection and can help improve the understanding of maize resistance to gray leaf spot.

MaizeGDB: The Maize Genetics and Genomics Database

MaizeGDB is the community database for biological information about the crop plant Zea mays. Genomic, genetic, sequence, gene product, functional characterization, literature reference, and person/organization contact information are among the datatypes stored at MaizeGDB. At the project's website ( http://www.maizegdb.org ) are custom interfaces enabling researchers to browse data and to seek out specific information matching explicit search criteria. In addition, pre-compiled reports are made available for particular types of data and bulletin boards are provided to facilitate communication and coordination among members of the community of maize geneticists.

MaizeGDB update: new tools, data and interface for the maize model organism database

MaizeGDB is a highly curated, community-oriented database and informatics service to researchers focused on the crop plant and model organism Zea mays ssp. mays. Although some form of the maize community database has existed over the last 25 years, there have only been two major releases. In 1991, the original maize genetics database MaizeDB was created. In 2003, the combined contents of MaizeDB and the sequence data from ZmDB were made accessible as a single resource named MaizeGDB. Over the next decade, MaizeGDB became more sequence driven while still maintaining traditional maize genetics datasets. This enabled the project to meet the continued growing and evolving needs of the maize research community, yet the interface and underlying infrastructure remained unchanged. In 2015, the MaizeGDB team completed a multi-year effort to update the MaizeGDB resource by reorganizing existing data, upgrading hardware and infrastructure, creating new tools, incorporating new data types (including diversity data, expression data, gene models, and metabolic pathways), and developing and deploying a modern interface. In addition to coordinating a data resource, the MaizeGDB team coordinates activities and provides technical support to the maize research community. MaizeGDB is accessible online at http://www.maizegdb.org.

Transformation of rice with large maize genomic DNA fragments containing high content repetitive sequences

Large and complex maize BIBAC inserts, even with a length of about 164 kb and repeat sequences of 88.1%, were transferred into rice. The BIBAC vector has been established to clone large DNA fragments and directly transfer them into plants. Previously, we have constructed a maize B73 BIBAC library and demonstrated that the BIBAC clones were stable in Agrobacterium. In this study, we demonstrated that the maize BIBAC clones could be used for rice genetic transformation through Agrobacterium-mediated method, although the average transformation efficiency for the BIBAC clones (0.86%) is much lower than that for generally used binary vectors containing small DNA fragments (15.24%). The 164-kb B73 genomic DNA insert of the BIBAC clone B2-6 containing five maize gene models and 88.1% of repetitive sequences was transferred into rice. In 18.75% (3/16) of the T1, 13.79% (4/29) of the T2, and 5.26% (1/19) of the T3 generation transgenic rice plants positive for the GUS and HYG marker genes, all the five maize genes can be detected. To our knowledge, this is the largest and highest content of repeat sequence-containing DNA fragment that was successfully transferred into plants. Gene expression analysis (RT-PCR) showed that the expression of three out of five genes could be detected in the leaves of the transgenic rice plants. Our study showed a potential to massively use maize genome resource for rice breeding by mass transformation of rice with large maize genomic DNA fragment BIBAC clones.

Genome-wide association study reveals a set of genes associated with resistance to the Mediterranean corn borer (Sesamia nonagrioides L.) in a maize diversity panel

BACKGROUND

Corn borers are the primary maize pest; their feeding on the pith results in stem damage and yield losses. In this study, we performed a genome-wide association study (GWAS) to identify SNPs associated with resistance to Mediterranean corn borer in a maize diversity panel using a set of more than 240,000 SNPs.

RESULTS

Twenty five SNPs were significantly associated with three resistance traits: 10 were significantly associated with tunnel length, 4 with stem damage, and 11 with kernel resistance. Allelic variation at each significant SNP was associated with from 6 to 9% of the phenotypic variance. A set of genes containing or physically close to these SNPs are proposed as candidate genes for borer resistance, supported by their involvement in plant defense-related mechanisms in previously published evidence. The linkage disequilibrium decayed (r(2) < 0.10) rapidly within short distance, suggesting high resolution of GWAS associations.

CONCLUSIONS

Most of the candidate genes found in this study are part of signaling pathways, others act as regulator of expression under biotic stress condition, and a few genes are encoding enzymes with antibiotic effect against insects such as the cystatin1 gene and the defensin proteins. These findings contribute to the understanding the complex relationship between plant-insect interactions.