Genetic variation in ZmVPP1 contributes to drought tolerance in maize seedlings

Digging for Stress-Responsive Cell Wall Proteins for Developing Stress-Resistant Maize

As a vital component of plant cell walls, proteins play important roles in stress response by modifying the structure of cell walls and involving in the wall integrity signaling pathway. Recently, we have critically reviewed the predictors, databases, and cross-referencing of the subcellular locations of possible cell wall proteins (CWPs) in plants (Briefings in Bioinformatics 2018;19:1130-1140). Here, we briefly introduce strategies for isolating CWPs during proteomic analysis. Taking maize (Zea mays) as an example, we retrieved 1873 probable maize CWPs recorded in the UniProt KnowledgeBase (UniProtKB). After curation, 863 maize CWPs were identified and classified into 59 kinds of protein families. By referring to gene ontology (GO) annotations and gene differential expression in the Expression Atlas, we have highlighted the potential of CWPs acting in the front line of defense against biotic and abiotic stresses. Moreover, the analysis results of cis-acting elements revealed the responsiveness of the genes encoding CWPs toward phytohormones and various stresses. We suggest that the stress-responsive CWPs could be promising candidates for applications in developing varieties of stress-resistant maize.

RING finger ubiquitin E3 ligase gene TaSDIR1-4A contributes to determination of grain size in common wheat

Salt and drought-induced RING finger1 (SDIR1) is a RING-type E3 ubiquitin ligase that plays a key role in ABA-mediated responses to salinity and drought stress via the ubiquitination pathway in some plant species. However, its function in wheat (Triticum aestivum) is unknown. Here, we isolated a SDIR1 member in wheat, TaSDIR1-4A, and characterized its E3 ubiquitin ligase activity. DNA polymorphism assays showed the presence of two nucleotide variation sites in the promoter region of TaSDIR1-4A, leading to the detection of the haplotypes Hap-4A-1 and Hap-4A-2 in wheat populations. Association analysis showed that TaSDIR1-4A haplotypes were associated with 1000-grain weight (TGW) across a variety of different environments, including well-watered and heat-stress conditions. Genotypes with Hap-4A-2 had higher TGW than those with Hap-4A-1. Phenotypes in both gene-silenced wheat and transgenic Arabidopsis showed that TaSDIR1-4A was a negative regulator of grain size. Gene expression assays indicated that TaSDIR1-4A was most highly expressed in flag leaves, and expression was higher in Hap-4A-1 accessions than in Hap-4A-2 accessions. The difference might be attributable to the fact that TaERF3 (ethylene response factor) can act as a transcriptional repressor of TaSDIR1-4A in Hap-4A-2 but not in Hap-4A-1. Examination of modern wheat varieties shows that the favorable haplotype has been positively selected in breeding programs in China. The functional marker for TaSDIR1-4A developed in this study should be helpful for future wheat breeding.

Necrotic upper tips1 mimics heat and drought stress and encodes a protoxylem-specific transcription factor in maize

Maintaining sufficient water transport during flowering is essential for proper organ growth, fertilization, and yield. Water deficits that coincide with flowering result in leaf wilting, necrosis, tassel browning, and sterility, a stress condition known as "tassel blasting." We identified a mutant, necrotic upper tips1 (nut1), that mimics tassel blasting and drought stress and reveals the genetic mechanisms underlying these processes. The nut1 phenotype is evident only after the floral transition, and the mutants have difficulty moving water as shown by dye uptake and movement assays. These defects are correlated with reduced protoxylem vessel thickness that indirectly affects metaxylem cell wall integrity and function in the mutant. nut1 is caused by an Ac transposon insertion into the coding region of a unique NAC transcription factor within the VND clade of Arabidopsis NUT1 localizes to the developing protoxylem of root, stem, and leaf sheath, but not metaxylem, and its expression is induced by flowering. NUT1 downstream target genes function in cell wall biosynthesis, apoptosis, and maintenance of xylem cell wall thickness and strength. These results show that maintaining protoxylem vessel integrity during periods of high water movement requires the expression of specialized, dynamically regulated transcription factors within the vasculature.

The Polymorphism of LvMMD2 and Its Association with Growth Traits in Litopenaeus vannamei

The Pacific white shrimp Litopenaeus vannamei is one of the major economic aquaculture species. The growth trait is considered as the most important trait in L. vannamei aquaculture. Identification of the genetic components underlying growth-related traits in L. vannamei could be useful for the selective breeding of growth trait. Our previous work identified several growth-related SNPs by genome-wide association study (GWAS). Based on the assembled genome, we identified a new candidate gene (LvMMD2) beside the associated marker. This gene encodes the progestin and AdipoQ receptor 10 (PAQR10) protein. We further investigate the polymorphisms of LvMMD2 and their association with body weight of L. vannamei. By resequencing the coding region of LvMMD2, a total of 8 SNPs were identified, including 6 synonymous mutations and 2 nonsynonymous mutations. Association analyses based on a population of 322 individuals revealed that several SNPs located in the coding region of LvMMD2 were significantly associated with the body weight, especially the nonsynonymous mutation named as MMD_5 contributed the most association to the trait and it could explain 10.5% of phenotypic variance. In addition, several genes involved in growth and development have been identified as LvMMD2-interacting genes. These findings strongly suggested that LvMMD2 might be an important gene regulating the shrimp growth. More importantly, the MMD_5 could be a promising candidate locus for marker-assisted selection (MAS) of the body weight in L. vannamei.

Genetic variants and underlying mechanisms influencing variance heterogeneity in maize

Traditional genetic studies focus on identifying genetic variants associated with the mean difference in a quantitative trait. Because genetic variants also influence phenotypic variation via heterogeneity, we conducted a variance-heterogeneity genome-wide association study to examine the contribution of variance heterogeneity to oil-related quantitative traits. We identified 79 unique variance-controlling single nucleotide polymorphisms (vSNPs) from the sequences of 77 candidate variance-heterogeneity genes for 21 oil-related traits using the Levene test (P < 1.0 × 10^-5 ). About 30% of the candidate genes encode enzymes that work in lipid metabolic pathways, most of which define clear expression variance quantitative trait loci. Of the vSNPs specifically associated with the genetic variance heterogeneity of oil concentration, 89% can be explained by additional linked mean-effects genetic variants. Furthermore, we demonstrated that gene × gene interactions play important roles in the formation of variance heterogeneity for fatty acid compositional traits. The interaction pattern was validated for one gene pair (GRMZM2G035341 and GRMZM2G152328) using yeast two-hybrid and bimolecular fluorescent complementation analyses. Our findings have implications for uncovering the genetic basis of hidden additive genetic effects and epistatic interaction effects, and we indicate opportunities to stabilize efficient breeding and selection of high-oil maize (Zea mays L.).

Mapping regulatory variants controlling gene expression in drought response and tolerance in maize

BACKGROUND

Gene expression is a key determinant of cellular response. Natural variation in gene expression bridges genetic variation to phenotypic alteration. Identification of the regulatory variants controlling the gene expression in response to drought, a major environmental threat of crop production worldwide, is of great value for drought-tolerant gene identification.

RESULTS

A total of 627 RNA-seq analyses are performed for 224 maize accessions which represent a wide genetic diversity under three water regimes; 73,573 eQTLs are detected for about 30,000 expressing genes with high-density genome-wide single nucleotide polymorphisms, reflecting a comprehensive and dynamic genetic architecture of gene expression in response to drought. The regulatory variants controlling the gene expression constitutively or drought-dynamically are unraveled. Focusing on dynamic regulatory variants resolved to genes encoding transcription factors, a drought-responsive network reflecting a hierarchy of transcription factors and their target genes is built. Moreover, 97 genes are prioritized to associate with drought tolerance due to their expression variations through the Mendelian randomization analysis. One of the candidate genes, Abscisic acid 8'-hydroxylase, is verified to play a negative role in plant drought tolerance.

CONCLUSIONS

This study unravels the effects of genetic variants on gene expression dynamics in drought response which allows us to better understand the role of distal and proximal genetic effects on gene expression and phenotypic plasticity. The prioritized drought-associated genes may serve as direct targets for functional investigation or allelic mining.

Identification of drought tolerant mechanisms in a drought-tolerant maize mutant based on physiological, biochemical and transcriptomic analyses

BACKGROUND

Frequently occurring drought stress negatively affects the production of maize worldwide. Numerous efforts have been made to develop drought-tolerant maize lines and to explore drought tolerant mechanisms in maize. However, there is a lack of comparative studies on transcriptomic changes between drought-tolerant and control maize lines.

RESULTS

In the present study, we have developed a drought-tolerant maize mutant (C7-2t) by irradiating the seeds of maize inbred line ChangC7-2 (C7-2) with ⁶⁰Co-γ. Compared to its wild type C7-2, C7-2t exhibited a significantly delayed wilting and higher drought tolerance under both the controlled and field conditions, indicating its high water-holding ability. Transcriptomic profiling was performed to identify differentially expressed genes (DEGs) between C7-2 and C7-2t during drought. As a result, a total of 4552 DEGs were implied in drought tolerance of C7-2 and C7-2t. In particular, the expression of photosynthesis-related genes in C7-2 was inhibited, whereas these genes in C7-2t were almost unaffected under drought. Moreover, a specific set of the DEGs were involved in phenylpropanoid biosynthesis and taurine (hypotaurine) metabolism in C7-2t; these DEGs were enriched in cell components associated with membrane systems and cell wall biosynthesis.

CONCLUSIONS

The drought tolerance of C7-2t was largely due to its high water-holding ability, stable photosynthesis (for supporting osmoregulation) and strengthened biosynthesis of cell walls under drought conditions.

Root architecture and hydraulics converge for acclimation to changing water availability

Because of intense transpiration and growth, the needs of plants for water can be immense. Yet water in the soil is most often heterogeneous if not scarce due to more and more frequent and intense drought episodes. The converse context, flooding, is often associated with marked oxygen deficiency and can also challenge the plant water status. Under our feet, roots achieve an incredible challenge to meet the water demand of the plant's aerial parts under such dramatically different environmental conditions. For this, they continuously explore the soil, building a highly complex, branched architecture. On shorter time scales, roots keep adjusting their water transport capacity (their so-called hydraulics) locally or globally. While the mechanisms that directly underlie root growth and development as well as tissue hydraulics are being uncovered, the signalling mechanisms that govern their local and systemic adjustments as a function of water availability remain largely unknown. A comprehensive understanding of root architecture and hydraulics as a whole (in other terms, root hydraulic architecture) is needed to apprehend the strategies used by plants to optimize water uptake and possibly improve crops regarding this crucial trait.

Genetic basis and identification of candidate genes for salt tolerance in rice by GWAS

Soil salinity is a major factor affecting rice growth and productivity worldwide especially at seedling stage. Many genes for salt tolerance have been identified and applied to rice breeding, but the actual mechanism of salt tolerance remains unclear. In this study, seedlings of 664 cultivated rice varieties from the 3000 Rice Genome Project (3K-RG) were cultivated by hydroponic culture with 0.9% salt solution for trait identification. A genome-wide association study (GWAS) of salt tolerance was performed using different models of analysis. Twenty-one QTLs were identified and two candidate genes named OsSTL1 (Oryza sativa salt tolerance level 1) and OsSTL2 (Oryza sativa salt tolerance level 2) were confirmed using sequence analysis. Haplotype and sequence analysis revealed that gene OsSTL1 was a homolog of salt tolerance gene SRP1 (Stress associated RNA-binding protein 1) in Arabidopsis. The hap1 of OsSTL1 was identified as the superior haplotype and a non-synonymous SNP was most likely to be the functional site. We also determined that the level of salt tolerance was improved by combining haplotypes of different genes. Our study provides a foundation for molecular breeding and functional analysis of salt tolerance in rice seedlings.

Genetic basis and identification of candidate genes for salt tolerance in rice by GWAS

Soil salinity is a major factor affecting rice growth and productivity worldwide especially at seedling stage. Many genes for salt tolerance have been identified and applied to rice breeding, but the actual mechanism of salt tolerance remains unclear. In this study, seedlings of 664 cultivated rice varieties from the 3000 Rice Genome Project (3K-RG) were cultivated by hydroponic culture with 0.9% salt solution for trait identification. A genome-wide association study (GWAS) of salt tolerance was performed using different models of analysis. Twenty-one QTLs were identified and two candidate genes named OsSTL1 (Oryza sativa salt tolerance level 1) and OsSTL2 (Oryza sativa salt tolerance level 2) were confirmed using sequence analysis. Haplotype and sequence analysis revealed that gene OsSTL1 was a homolog of salt tolerance gene SRP1 (Stress associated RNA-binding protein 1) in Arabidopsis. The hap1 of OsSTL1 was identified as the superior haplotype and a non-synonymous SNP was most likely to be the functional site. We also determined that the level of salt tolerance was improved by combining haplotypes of different genes. Our study provides a foundation for molecular breeding and functional analysis of salt tolerance in rice seedlings.

Dissection of the genetic basis of oil content in Chinese peanut cultivars through association mapping

Background

Peanut is one of the primary sources for vegetable oil worldwide, and enhancing oil content is the main objective in several peanut breeding programs of the world. Tightly linked markers are required for faster development of high oil content peanut varieties through genomics-assisted breeding (GAB), and association mapping is one of the promising approaches for discovery of such associated markers.

Results

An association mapping panel consisting of 292 peanut varieties extensively distributed in China was phenotyped for oil content and genotyped with 583 polymorphic SSR markers. These markers amplified 3663 alleles with an average of 6.28 alleles per locus. The structure, phylogenetic relationship, and principal component analysis (PCA) indicated two subgroups majorly differentiating based on geographic regions. Genome-wide association analysis identified 12 associated markers including one (AGGS1014_2) highly stable association controlling up to 9.94% phenotypic variance explained (PVE) across multiple environments. Interestingly, the frequency of the favorable alleles for 12 associated markers showed a geographic difference. Two associated markers (AGGS1014_2 and AHGS0798) with 6.90–9.94% PVE were verified to enhance oil content in an independent RIL population and also indicated selection during the breeding program.

Conclusion

This study provided insights into the genetic basis of oil content in peanut and verified highly associated two SSR markers to facilitate marker-assisted selection for developing high-oil content breeding peanut varieties.

Genome-wide association study leads to novel genetic insights into resistance to Aspergillus flavus in maize kernels

BACKGROUND

Fungus infection in staple grains affects the food storage and threatens food security. The Aspergillus flavus is known to infect multiple grains and produce mycotoxin Aflatoxin B1, which is mutagenic, teratogenic and causes immunosuppression in animals. However, the molecular mechanism of maize resistance to A. flavus is largely unknown.

RESULTS

Here we used corn kernels to investigate resistance genes to A. flavus using genome-wide association study (GWAS) of 313 inbred lines. We characterized the resistance levels of kernels after inoculating with A. flavus. The GWAS with 558,529 SNPs identified four associated loci involving 29 candidate genes that were linked to seed development, resistance or infection, and involved in signal pathways, seed development, germination, dormancy, epigenetic modification, and antimicrobial activity. In addition, a few candidate genes were also associated with several G-protein signaling and phytohormones that might involve in synergistic work conferring different resistance during seed development. Expression of 16 genes out of 29 during kernel development was also associated with resistance levels.

CONCLUSIONS

We characterized the resistance levels of 313 maize kernels after inoculating with A. flavus, and found four associated loci and 16 candidate maize genes. The expressed 16 genes involved in kernel structure and kernel composition most likely contribute to mature maize kernels' resistance to A. flavus, and in particular, in the development of pericarp. The linked candidate genes could be experimentally transformed to validate and manipulate fungal resistance. Thus this result adds value to maize kernels in breeding programs.

Early Drought-Responsive Genes Are Variable and Relevant to Drought Tolerance

Drought stress is an important crop yield limiting factor worldwide. Plant physiological responses to drought stress are driven by changes in gene expression. While drought-responsive genes (DRGs) have been identified in maize, regulation patterns of gene expression during progressive water deficits remain to be elucidated. In this study, we generated time-series transcriptomic data from the maize inbred line B73 under well-watered and drought conditions. Comparisons between the two conditions identified 8,626 DRGs and the stages (early, middle, and late drought) at which DRGs occurred. Different functional groups of genes were regulated at the three stages. Specifically, early and middle DRGs display higher copy number variation among diverse Zea mays lines, and they exhibited stronger associations with drought tolerance as compared to late DRGs. In addition, correlation of expression between small RNAs (sRNAs) and DRGs from the same samples identified 201 negatively sRNA/DRG correlated pairs, including genes showing high levels of association with drought tolerance, such as two glutamine synthetase genes, gln2 and gln6 The characterization of dynamic gene responses to progressive drought stresses indicates important adaptive roles of early and middle DRGs, as well as roles played by sRNAs in gene expression regulation upon drought stress.

Genetic variation in ZmTIP1 contributes to root hair elongation and drought tolerance in maize

Drought is a major abiotic stress that threatens maize production globally. A previous genome-wide association study identified a significant association between the natural variation of ZmTIP1 and the drought tolerance of maize seedlings. Here, we report on comprehensive genetic and functional analysis, indicating that ZmTIP1, which encodes a functional S-acyltransferase, plays a positive role in regulating the length of root hairs and the level of drought tolerance in maize. We show that enhancing ZmTIP1 expression in transgenic Arabidopsis and maize increased root hair length, as well as plant tolerance to water deficit. In contrast, ZmTIP1 transposon-insertional mutants displayed the opposite phenotype. A calcium-dependent protein kinase, ZmCPK9, was identified as a substrate protein of ZmTIP1, and ZmTIP1-mediated palmitoylation of two cysteine residues facilitated the ZmCPK9 PM association. The results of this research enrich our knowledge about ZmTIP1-mediated protein S-acylation modifications in relation to the regulation of root hair elongation and drought tolerance. Additionally, the identification of a favourable allele of ZmTIP1 also provides a valuable genetic resource or selection target for the genetic improvement of maize.

Genome optimization for improvement of maize breeding

We propose a new model to improve maize breeding that incorporates doubled haploid production, genomic selection, and genome optimization. Breeding 4.0 has been considered the next era of plant breeding. It is clear that the Breeding 4.0 era for maize will feature the integration of multi-disciplinary technologies including genomics and phenomics, gene editing and synthetic biology, and Big Data and artificial intelligence. The breeding approach of passively selecting ideal genotypes from designated genetic pools must soon evolve to virtual design of optimized genomes by pyramiding superior alleles using computational simulation. An optimized genome expressing optimal phenotypes, which may never actually be created, can function as a blueprint for breeding programs to use minimal materials and hybridizations to achieve maximum genetic gain. We propose a new breeding pipeline, "genomic design breeding," that incorporates doubled haploid production, genomic selection, and genome optimization and is facilitated by different scales of trait predictions and decision-making models. Successful implementation of the proposed model will facilitate the evolution of maize breeding from "art" to "science" and eventually to "intelligence," in the Breeding 4.0 era.

Transcription factors as molecular switches to regulate drought adaptation in maize

Here, we reviewed major transcription factors of maize that confer drought stress tolerance, and their target genes and involved signaling pathway. Transcription factors in maize can be promising candidates for improving comprehensive resistance of multiple environmental stimuli. Adverse environmental stress is the main influencing factor affecting plant growth and reproduction, which poses tremendous threats to sustainable agriculture development and crops productivity worldwide. Among various abiotic stress factors, drought is the most vital adversity with the characteristics of frequent occurrences, long duration, and globality. Maize (Zea mays L.) is a major source of food supply for human being and livestock and recently for biofuel. Maize is the crop that is highly susceptible to drought stress. Drought stress tolerance in plants is quite complex, and it is not ideal to improve crop drought tolerance through a single resistant gene. Transcription factors participate in the regulation of plant growth and development, morphogenesis, and various environmental stress responses via regulating the expression level of their target stress-responsive genes independently or cross talk with other transcription factors, thereby the comprehensive resistance of multiple stresses in crops is improved. This review aims to summarize the major drought-tolerant transcription factors in maize and their regulatory network. With the continuous identification of maize transcription factors, more will be demonstrated to confer drought tolerance either in maize or other crops. It is expected that the transcription factors will greatly enrich the functional gene resources and will be a benefit to drought-tolerant maize cultivars breeding.

GWAS and co-expression network combination uncovers multigenes with close linkage effects on the oleic acid content accumulation in Brassica napus

Background

Strong artificial and natural selection causes the formation of highly conserved haplotypes that harbor agronomically important genes. GWAS combination with haplotype analysis has evolved as an effective method to dissect the genetic architecture of complex traits in crop species.

Results

We used the 60 K Brassica Infinium SNP array to perform a genome-wide analysis of haplotype blocks associated with oleic acid (C18:1) in rapeseed. Six haplotype regions were identified as significantly associated with oleic acid (C18:1) that mapped to chromosomes A02, A07, A08, C01, C02, and C03. Additionally, whole-genome sequencing of 50 rapeseed accessions revealed three genes (BnmtACP2-A02, BnABCI13-A02 and BnECI1-A02) in the A02 chromosome haplotype region and two genes (BnFAD8-C02 and BnSDP1-C02) in the C02 chromosome haplotype region that were closely linked to oleic acid content phenotypic variation. Moreover, the co-expression network analysis uncovered candidate genes from these two different haplotype regions with potential regulatory interrelationships with oleic acid content accumulation.

Conclusions

Our results suggest that several candidate genes are closely linked, which provides us with an opportunity to develop functional haplotype markers for the improvement of the oleic acid content in rapeseed.

Sulfur-enriched leonardite and humic acid soil amendments enhance tolerance to drought and phosphorus deficiency stress in maize (Zea mays L.)

Soil amendments are known to promote several plant growth parameters. In many agro-ecosystems, water scarcity and drought induced phosphorus deficiency limits crop yield significantly. Considering the climate change scenario, drought and related stress factors will be even more severe endangering the global food security. Therefore, two parallel field trials were conducted to examine at what extent soil amendment of leonardite and humic acid would affect drought and phosphorus tolerance of maize. The treatments were: control (C: 100% A pan and 125 kg P ha⁻¹), P deficiency (phosphorus stress (PS): 62.5 kg P ha⁻¹), water deficit stress (water stress (WS): 67% A pan), and PS + WS (67% A pan and 62.5 kg P ha⁻¹). Three organic amendments were (i) no amendment, (ii) 625 kg S + 750 kg leonardite ha⁻¹ and (iii) 1250 kg S + 37.5 kg humic acid ha⁻¹) tested on stress treatments. Drought and P deficiency reduced plant biomass, grain yield, chlorophyll content, F_v/F_m, RWC and antioxidant activity (superoxide dismutase, peroxidase, and catalase), but increased electrolyte leakage and leaf H₂O₂ in maize plants. The combined stress of drought and P deficiency decreased further related plant traits. Humic acid and leonardite enhanced leaf P and yield in maize plants under PS. A significant increase in related parameters was observed with humic acid and leonardite under WS. The largest increase in yield and plant traits in relation to humic acid and leonardite application was observed under combined stress situation. The use of sulfur-enriched amendments can be used effectively to maintain yield of maize crop in water limited calcareous soils.

Regulatory changes in TaSNAC8-6A are associated with drought tolerance in wheat seedlings

Wheat is a staple crop produced in arid and semi-arid areas worldwide, and its production is frequently compromised by water scarcity. Thus, increased drought tolerance is a priority objective for wheat breeding programmes, and among their targets, the NAC transcription factors have been demonstrated to contribute to plant drought response. However, natural sequence variations in these genes have been largely unexplored for their potential roles in drought tolerance. Here, we conducted a candidate gene association analysis of the stress-responsive NAC gene subfamily in a wheat panel consisting of 700 varieties collected worldwide. We identified a drought responsive gene, TaSNAC8-6A, that is tightly associated with drought tolerance in wheat seedlings. Further analysis found that a favourable allele TaSNAC8-6A^In-313 , carrying an insertion in the ABRE promoter motif, is targeted by TaABFs and confers enhanced drought-inducible expression of TaSNAC8-6A in drought-tolerant genotypes. Transgenic wheat and Arabidopsis TaSNAC8-6A overexpression lines exhibited enhanced drought tolerance through induction of auxin- and drought-response pathways, confirmed by transcriptomic analysis, that stimulated lateral root development, subsequently improving water-use efficiency. Taken together, our findings reveal that natural variation in TaSNAC8-6A and specifically the TaSNAC8-6A^In-313 allele strongly contribute to wheat drought tolerance and thus represent a valuable genetic resource for improvement of drought-tolerant germplasm for wheat production.

IntAssoPlot: An R Package for Integrated Visualization of Genome-Wide Association Study Results With Gene Structure and Linkage Disequilibrium Matrix

Genome-wide association study (GWAS), exploring the historical and evolutionary recombinations at the population level, is a major method adopted to identify quantitative trait loci (QTL) for complex traits. However, to summarize GWAS results, gene structure, and linkage disequilibrium (LD) in a single view, multiple tools are required. It is tedious to generate these three results and manually put them together; moreover, it may eventually lead to inaccuracies. On the other hand, genotype markers are usually detected by DNA- and/or RNA-Seq. For GWAS analysis based on RNA-Seq, markers from DNA-Seq provide more genetic information when displaying LD. The currently released software package does not have this function for an integrated analysis of LD, using genotypic markers different from that in association analysis. Here, we present an R package, IntAssoPlot, which provides an integrated visual display of GWAS results, along with LD and gene structure information, in a publication-ready format. The main panel of an IntAssoPlot plot has a connecting line linking the genome-wide association P-values on the -log10 scale with the gene structure and LD matrix. Importantly, IntAssoPlot is designed to plot GWAS results with LD calculated from genotypes different from those in GWAS analysis. IntAssoPlot provides a powerful visualization tool to gain an integrated insight into GWAS results. The functions provided by IntAssoPlot increase the efficiency by revealing GWAS results in a publication-ready format. Inspection of the output image can provide important biological information, including the loci that passed the genome-wide significance threshold, genes located at or near the significant loci, and the extent of LD within the selected region.

Mapping-by-Sequencing via MutMap Identifies a Mutation in ZmCLE7 Underlying Fasciation in a Newly Developed EMS Mutant Population in an Elite Tropical Maize Inbred

Induced point mutations are important genetic resources for their ability to create hypo- and hypermorphic alleles that are useful for understanding gene functions and breeding. However, such mutant populations have only been developed for a few temperate maize varieties, mainly B73 and W22, yet no tropical maize inbred lines have been mutagenized and made available to the public to date. We developed a novel Ethyl Methanesulfonate (EMS) induced mutation resource in maize comprising 2050 independent M2 mutant families in the elite tropical maize inbred ML10. By phenotypic screening, we showed that this population is of comparable quality with other mutagenized populations in maize. To illustrate the usefulness of this population for gene discovery, we performed rapid mapping-by-sequencing to clone a fasciated-ear mutant and identify a causal promoter deletion in ZmCLE7 (CLE7). Our mapping procedure does not require crossing to an unrelated parent, thus is suitable for mapping subtle traits and ones affected by heterosis. This first EMS population in tropical maize is expected to be very useful for the maize research community. Also, the EMS mutagenesis and rapid mapping-by-sequencing pipeline described here illustrate the power of performing forward genetics in diverse maize germplasms of choice, which can lead to novel gene discovery due to divergent genetic backgrounds.

Excess Pyrophosphate Restrains Pavement Cell Morphogenesis and Alters Organ Flatness in Arabidopsis thaliana

In Arabidopsis thaliana, the vacuolar proton-pumping pyrophosphatase (H⁺-PPase) is highly expressed in young tissues, which consume large amounts of energy in the form of nucleoside triphosphates and produce pyrophosphate (PPi) as a byproduct. We reported that excess PPi in the H⁺-PPase loss-of-function fugu5 mutant severely compromised gluconeogenesis from seed storage lipids, arrested cell division in cotyledonary palisade tissue, and triggered compensated cell enlargement; this phenotype was recovered upon sucrose supply. Thus, we provided evidence that the hydrolysis of inhibitory PPi, rather than vacuolar acidification, is the major contribution of H⁺-PPase during seedling establishment. Here, examination of the epidermis revealed that fugu5 pavement cells exhibited defective puzzle-cell formation. Importantly, removal of PPi from fugu5 background by the yeast cytosolic PPase IPP1, in fugu5-1 AVP1_pro::IPP1 transgenic lines, restored the phenotypic aberrations of fugu5 pavement cells. Surprisingly, pavement cells in mutants with defects in gluconeogenesis (pck1-2) or the glyoxylate cycle (icl-2; mls-2) showed no phenotypic alteration, indicating that reduced sucrose production from seed storage lipids is not the cause of fugu5 epidermal phenotype. fugu5 had oblong cotyledons similar to those of angustifolia-1 (an-1), whose leaf pavement cells display an abnormal arrangement of cortical microtubules (MTs). To gain insight into the genetic interaction between ANGUSTIFOLIA and H⁺-PPase in pavement cell differentiation, an-1 fugu5-1 was analyzed. Surprisingly, epidermis developmental defects were synergistically enhanced in the double mutant. In fact, an-1 fugu5-1 pavement cells showed a striking three-dimensional growth phenotype on both abaxial and adaxial sides of cotyledons, which was recovered by hydrolysis of PPi in an-1 fugu5-1 AVP1_pro::IPP1. Live imaging revealed that cortical MTs exhibited a reduced velocity, were slightly fragmented and sparse in the above lines compared to the WT. Consistently, addition of PPi in vitro led to a dose-dependent delay of tubulin polymerization, thus supporting a link between PPi and MT dynamics. Moreover, mathematical simulation of three-dimensional growth based on cotyledon proximo-distal and medio-lateral phenotypic quantification implicated restricted cotyledon expansion along the medio-lateral axis in the crinkled surface of an-1 fugu5-1. Together, our data suggest that PPi homeostasis is a prerequisite for proper pavement cell morphogenesis, epidermal growth and development, and organ flattening.

Identifying Vitamin E Biosynthesis Genes in Elaeis guineensis by Genome-Wide Association Study

Elaeis guineensis is a tropical oil crop and has the highest oil yield per unit area. Palm oil has high palmitic acid content and is also rich in vitamins, including vitamin E. We conducted genome-wide association studies in a diversity panel of 161 E. guineensis accessions to identify single-nucleotide polymorphisms (SNPs) linked with vitamin E and validated candidate genes in these marker-associated intervals. Based on the SNPs reported in our previous research, 47 SNP markers were detected to be significantly associated with the variation of tocopherol and tocotrienol content at a cutoff P value of 6.3 × 10^-7. A total of 656 candidate genes in the flanking regions of the 47 SNPs were identified, followed by pathway enrichment analysis. Of these candidate genes, EgHGGT (homogentisate geranylgeranyl transferase) involved in the biosynthesis of tocotrienols had a higher expression level in the mesocarp compared to other tissues. Expression of the EgHGGT gene was positively correlated with the variation in α-tocotrienol content. Induced overexpression of the gene in Arabidopsis caused a significant increase in vitamin E content and production of α-tocotrienols compared to wild Arabidopsis.

The Past, Present, and Future of Maize Improvement: Domestication, Genomics, and Functional Genomic Routes toward Crop Enhancement

After being domesticated from teosinte, cultivated maize (Zea mays ssp. mays) spread worldwide and now is one of the most important staple crops. Due to its tremendous phenotypic and genotypic diversity, maize also becomes to be one of the most widely used model plant species for fundamental research, with many important discoveries reported by maize researchers. Here, we provide an overview of the history of maize domestication and key genes controlling major domestication-related traits, review the currently available resources for functional genomics studies in maize, and discuss the functions of most of the maize genes that have been positionally cloned and can be used for crop improvement. Finally, we provide some perspectives on future directions regarding functional genomics research and the breeding of maize and other crops.

Plant Membrane Transport Research in the Post-genomic Era

Membrane transport processes are indispensable for many aspects of plant physiology including mineral nutrition, solute storage, cell metabolism, cell signaling, osmoregulation, cell growth, and stress responses. Completion of genome sequencing in diverse plant species and the development of multiple genomic tools have marked a new era in understanding plant membrane transport at the mechanistic level. Genes coding for a galaxy of pumps, channels, and carriers that facilitate various membrane transport processes have been identified while multiple approaches are developed to dissect the physiological roles as well as to define the transport capacities of these transport systems. Furthermore, signaling networks dictating the membrane transport processes are established to fully understand the regulatory mechanisms. Here, we review recent research progress in the discovery and characterization of the components in plant membrane transport that take advantage of plant genomic resources and other experimental tools. We also provide our perspectives for future studies in the field.

A class B heat shock factor selected for during soybean domestication contributes to salt tolerance by promoting flavonoid biosynthesis

Soybean (Glycine max) production is severely affected in unfavorable environments. Identification of the regulatory factors conferring stress tolerance would facilitate soybean breeding. In this study, through coexpression network analysis of salt-tolerant wild soybeans, together with molecular and genetic approaches, we revealed a previously unidentified function of a class B heat shock factor, HSFB2b, in soybean salt stress response. We showed that HSFB2b improves salt tolerance through the promotion of flavonoid accumulation by activating one subset of flavonoid biosynthesis-related genes and by inhibiting the repressor gene GmNAC2 to release another subset of genes in the flavonoid biosynthesis pathway. Moreover, four promoter haplotypes of HSFB2b were identified from wild and cultivated soybeans. Promoter haplotype II from salt-tolerant wild soybean Y20, with high promoter activity under salt stress, is probably selected for during domestication. Another promoter haplotype, III, from salt-tolerant wild soybean Y55, had the highest promoter activity under salt stress, had a low distribution frequency and may be subjected to the next wave of selection. Together, our results revealed the mechanism of HSFB2b in soybean salt stress tolerance. Its promoter variations were identified, and the haplotype with high activity may be adopted for breeding better soybean cultivars that are adapted to stress conditions.

A MYB-related transcription factor from sheepgrass, LcMYB2, promotes seed germination and root growth under drought stress

BACKGROUND

Drought is one of the most serious factors limiting plant growth and production. Sheepgrass can adapt well to various adverse conditions, including drought. However, during germination, sheepgrass young seedlings are sensitive to these adverse conditions. Therefore, the adaptability of seedlings is very important for plant survival, especially in plants that inhabit grasslands or the construction of artificial grassland.

RESULTS

In this study, we found a sheepgrass MYB-related transcription factor, LcMYB2 that is up-regulated by drought stress and returns to a basal level after rewatering. The expression of LcMYB2 was mainly induced by osmotic stress and was localized to the nucleus. Furthermore, we demonstrate that LcMYB2 promoted seed germination and root growth under drought and ABA treatments. Additionally, we confirmed that LcMYB2 can regulate LcDREB2 expression in sheepgrass by binding to its promoter, and it activates the expression of the osmotic stress marker genes AtDREB2A, AtLEA14 and AtP5CS1 by directly binding to their promoters in transgenic Arabidopsis.

CONCLUSIONS

Based on these results, we propose that LcMYB2 improves plant drought stress tolerance by increasing the accumulation of osmoprotectants and promoting root growth. Therefore, LcMYB2 plays pivotal roles in plant responses to drought stress and is an important candidate for genetic manipulation to create drought-resistant crops, especially during seed germination.

A group VII ethylene response factor gene, ZmEREB180, coordinates waterlogging tolerance in maize seedlings

Group VII ethylene response factors (ERFVIIs) play important roles in ethylene signalling and plant responses to flooding. However, natural ERFVII variations in maize (ZmERFVIIs) that are directly associated with waterlogging tolerance have not been reported. Here, a candidate gene association analysis of the ZmERFVII gene family showed that a waterlogging-responsive gene, ZmEREB180, was tightly associated with waterlogging tolerance. ZmEREB180 expression specifically responded to waterlogging and was up-regulated by ethylene; in addition, its gene product localized to the nucleus. Variations in the 5'-untranslated region (5'-UTR) and mRNA abundance of this gene under waterlogging conditions were significantly associated with survival rate (SR). Ectopic expression of ZmEREB180 in Arabidopsis increased the SR after submergence stress, and overexpression of ZmEREB180 in maize also enhanced the SR after long-term waterlogging stress, apparently through enhanced formation of adventitious roots (ARs) and regulation of antioxidant levels. Transcriptomic assays of the transgenic maize line under normal and waterlogged conditions further provided evidence that ZmEREB180 regulated AR development and reactive oxygen species homeostasis. Our study provides direct evidence that a ZmERFVII gene is involved in waterlogging tolerance. These findings could be applied directly to breed waterlogging-tolerant maize cultivars and improve our understanding of waterlogging stress.

TaARF4 genes are linked to root growth and plant height in wheat

BACKGROUND AND AIMS

Auxin response factors (ARFs) as transcription activators or repressors have important roles in plant growth and development, but knowledge about the functions of wheat ARF members is limited. A novel ARF member in wheat (Triticum aestivum), TaARF4, was identified, and its protein function, haplotype geographic distribution and allelic frequencies were investigated.

METHODS

Tissue expression of TaARF4 was analysed by real-time PCR. Sub-cellular localization was performed using green fluorescent protein (GFP)-tagged TaARF4. Ectopic expression of TaARF4-A in arabidopsis was used to study its functions. Electrophoretic mobility shift assays (EMSAs), chromatin immunoprecipitation (ChIP) analyses and gene expression were performed to detect TaARF4 target genes. A dCAPS (derived cleaved amplified polymorphic sequence) marker developed from TaARF4-B was used to identify haplotypes and association analysis between haplotypes and agronomic traits.

KEY RESULTS

TaARF4-A was constitutively expressed and its protein was localized in the nucleus. Ectopic expression of TaARF4-A in arabidopsis caused abscisic acid (ABA) insensitivity, shorter primary root length and reduced plant height (PH). Through expression studies and ChIP assays, TaARF4-A was shown to regulate HB33 expression which negatively responded to ABA, and reduced root length and plant height by repressing expression of Gretchen Hagen 3 (GH3) genes that in turn upregulated indole-3-acetic acid content in arabidopsis. Association analysis showed that TaARF4-B was strongly associated with PH and root depth at the tillering, jointing and grain fill stages. Geographic distribution and allelic frequencies suggested that TaARF4-B haplotypes were selected in Chinese wheat breeding programmes. An amino acid change (threonine to alanine) at position 158 might be the cause of phenotype variation in accessions possessing different haplotypes.

CONCLUSIONS

Ectopic expression and association analysis indicate that TaARF4 may be involved in root length and plant height determination in wheat. This work is helpful for selection of wheat genotypes with optimal root and plant architecture.

Genome-wide association study reveals genomic regions controlling root and shoot traits at late growth stages in wheat

BACKGROUND AND AIMS

Root system morphology is important for sustainable agriculture, but the genetic basis of root traits and their relationship to shoot traits remain to be elucidated. The aim of the present study was to dissect the genetic basis of root traits at late growth stages and its implications on shoot traits in wheat.

METHODS

Among 323 wheat accessions, we investigated phenotypic differences in root traits at booting and mid-grain fill stages in PVC tubes, shoot traits including plant height (PH), canopy temperature (CT) and grain yield per plant (YPP) in a field experiment, and performed a genome-wide association study with a Wheat 660K SNP Array.

KEY RESULTS

Deep-rooted accessions had lower CT and higher YPP than those with shallow roots, but no significant relationship was identified between root dry weight and shoot traits. Ninety-three significantly associated loci (SALs) were detected by the mixed linear model, among which three were hub SALs (Co-6A, Co-6B and Co-6D) associated with root depth at both booting and mid-grain fill stages, as well as CT and YPP. Minirhizotron system scanning results suggested that the causal genes in the three SALs may regulate root elongation in the field. The heritable independence between root depth and PH was demonstrated by linkage disequilibrium analysis. The YPP was significantly higher in genotypes which combined favourable marker alleles (FMAs) for root depth and PH, suggesting that a deep root and shorter plant height are suitable traits for pyramiding target alleles by molecular marker-assisted breeding.

CONCLUSIONS

These results uncovered promising genomic regions for functional gene discovery of root traits in the late growth period, enhanced understanding of correlation between root and shoot traits, and will facilitate intensive study on root morphology and breeding through molecular design.

Population-level analysis reveals the widespread occurrence and phenotypic consequence of DNA methylation variation not tagged by genetic variation in maize

BACKGROUND

DNA methylation can provide a source of heritable information that is sometimes entirely uncoupled from genetic variation. However, the extent of this uncoupling and the roles of DNA methylation in shaping diversity of both gene expression and phenotypes are hotly debated. Here, we investigate the genetic basis and biological functions of DNA methylation at a population scale in maize.

RESULTS

We perform targeted DNA methylation profiling for a diverse panel of 263 maize inbred genotypes. All genotypes show similar levels of DNA methylation globally, highlighting the importance of DNA methylation in maize development. Nevertheless, we identify more than 16,000 differentially methylated regions (DMRs) that are distributed across the 10 maize chromosomes. Genome-wide association analysis with high-density genetic markers reveals that over 60% of the DMRs are not tagged by SNPs, suggesting the presence of unique information in DMRs. Strong associations between DMRs and the expression of many genes are identified in both the leaf and kernel tissues, pointing to the biological significance of methylation variation. Association analysis with 986 metabolic traits suggests that DNA methylation is associated with phenotypic variation of 156 traits. There are some traits that only show significant associations with DMRs and not with SNPs.

CONCLUSIONS

These results suggest that DNA methylation can provide unique information to explain phenotypic variation in maize.

Natural variation in a calreticulin gene causes reduced resistance to Ca2+ deficiency-induced tipburn in Chinese cabbage (Brassica rapa ssp. pekinensis)

Tipburn is an irreversible physiological disorder of Chinese cabbage that decreases crop value. Because of a strong environmental component, tipburn-resistant cultivars are the only solution, although tipburn resistance genes are unknown in Chinese cabbage. We studied three populations of Chinese cabbage over four growing seasons under field conditions: (a) 194 diverse inbred lines, (b) a doubled haploid (DH100) population, and (c) an F₂ population. The 194 lines were genotyped using single nucleotide polymorphism markers, and genome-wide-association mapping showed that 24 gQTLs were significantly associated with tipburn disease index. Analysis of the DH100 and F₂ populations identified a shared tipburn-associated locus, gqbTRA06, that was found to cover the region defined by one of the 24 gQTLs. Of 35 genes predicted in the 0.14-Mb quantitative trait locus region, Bra018575 (calreticulin family protein, BrCRT2) showed higher expression levels during disease development. We cloned the two BrCRT2 alleles from tipburn-resistant (BrCRT2^R ) and tipburn-susceptible (BrCRT2^S ) lines and identified a 51-bp deletion in BrCRT2^S . Overexpression of BrCRT2^R increased Ca²⁺ storage in the Arabidopsis crt2 mutant and also reduced cell death in leaf tips and margins under Ca²⁺ -depleted conditions. Our results suggest that BrCRT2 is a possible candidate gene for controlling tipburn in Chinese cabbage.

Integrating GWAS and Gene Expression Analysis Identifies Candidate Genes for Root Morphology Traits in Maize at the Seedling Stage

Root system plays an essential role in water and nutrient acquisition in plants. Understanding the genetic basis of root development will be beneficial for breeding new cultivars with efficient root system to enhance resource use efficiency in maize. Here, the natural variation of 13 root and 3 shoot traits was evaluated in 297 maize inbred lines and genome-wide association mapping was conducted to identify SNPs associated with target traits. All measured traits exhibited 2.02- to 21.36-fold variations. A total of 34 quantitative trait loci (QTLs) were detected for 13 traits, and each individual QTL explained 5.7% to 15.9% of the phenotypic variance. Three pleiotropic QTLs involving five root traits were identified; SNP_2_104416607 was associated with lateral root length (LRL), root surface area (RA), root length between 0 and 0.5mm in diameter (RL005), and total root length (TRL); SNP_2_184016997 was associated with RV and RA, and SNP_4_168917747 was associated with LRL, RA and TRL. The expression levels of candidate genes in root QTLs were evaluated by RNA-seq among three long-root lines and three short-root lines. A total of five genes that showed differential expression between the long- and short-root lines were identified as promising candidate genes for the target traits. These QTLs and the potential candidate genes are important source data to understand root development and genetic improvement of root traits in maize.

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.

The genetic basis of drought tolerance in the high oil crop Sesamum indicum

Unlike most of the important food crops, sesame can survive drought but severe and repeated drought episodes, especially occurring during the reproductive stage, significantly curtail the productivity of this high oil crop. Genome-wide association study was conducted for traits related to drought tolerance using 400 diverse sesame accessions, including landraces and modern cultivars. Ten stable QTLs explaining more than 40% of the phenotypic variation and located on four linkage groups were significantly associated with drought tolerance related traits. Accessions from the tropical area harboured higher numbers of drought tolerance alleles at the peak loci and were found to be more tolerant than those from the northern area, indicating a long-term genetic adaptation to drought-prone environments. We found that sesame has already fixed important alleles conferring survival to drought which may explain its relative high drought tolerance. However, most of the alleles crucial for productivity and yield maintenance under drought conditions are far from been fixed. This study also revealed that pyramiding the favourable alleles observed at the peak loci is of high potential for enhancing drought tolerance in sesame. In addition, our results highlighted two important pleiotropic QTLs harbouring known and unreported drought tolerance genes such as SiABI4, SiTTM3, SiGOLS1, SiNIMIN1 and SiSAM. By integrating candidate gene association study, gene expression and transgenic experiments, we demonstrated that SiSAM confers drought tolerance by modulating polyamine levels and ROS homeostasis, and a missense mutation in the coding region partly contributes to the natural variation of drought tolerance in sesame.

Identification of Maize CC-Type Glutaredoxins That Are Associated with Response to Drought Stress

Global maize cultivation is often adversely affected by drought stress. The CC-type glutaredoxin (GRX) genes form a plant-specific subfamily that regulate plant growth and respond to environmental stresses. However, how maize CC-type GRX (ZmGRXCC) genes respond to drought stress remains unclear. We performed a TBLASTN search to identify ZmGRXCCs in the maize genome and verified the identified sequences using the NCBI conservative domain database (CDD). We further established a phylogenetic tree using Mega7 and surveyed known cis-elements in the promoters of ZmGRXCCs using the PlantCARE database. We found twenty-one ZmGRXCCs in the maize genome by a genome-wide investigation and compared their phylogenetic relationships with rice, maize, and Arabidopsis. The analysis of their redox active sites showed that most of the 21 ZmGRXCCs share similar structures with their homologs. We assessed their expression at young seedlings and adult leaves under drought stress and their expression profiles in 15 tissues, and found that they were differentially expressed, indicating that different ZmGRXCC genes have different functions. Notably, ZmGRXCC14 is up-regulated at seedling, V12, V14, V16, and R1 stages. Importantly, significant associations between genetic variation in ZmGRXCC14 and drought tolerance are found at the seedling stage. These results will help to advance the study of the function of ZmGRXCCs genes under drought stress and understand the mechanism of drought resistance in maize.

Analysis of Drought Tolerance and Associated Traits in Upland Cotton at the Seedling Stage

(1) Background: Upland cotton (Gossypium hirsutum L.) is the most important natural fiber worldwide, and it is extensively planted and plentifully used in the textile industry. Major cotton planting regions are frequently affected by abiotic stress, especially drought stress. Drought resistance is a complex, quantitative trait. A genome-wide association study (GWAS) constitutes an efficient method for dissecting the genetic architecture of complex traits. In this study, the drought resistance of a population of 316 upland cotton accessions was studied via GWAS. (2) Methods: GWAS methodology was employed to identify relationships between molecular markers or candidate genes and phenotypes of interest. (3) Results: A total of 8, 3, and 6 SNPs were associated with the euphylla wilting score (EWS), cotyledon wilting score (CWS), and leaf temperature (LT), respectively, based on a general linear model and a factored spectrally transformed linear mixed model. For these traits, 7 QTLs were found, of which 2 each were located on chromosomes A05, A11, and D03, and of which 1 was located on chromosome A01. Importantly, in the candidate regions WRKY70, GhCIPK6, SnRK2.6, and NET1A, which are involved in the response to abscisic acid (ABA), the mitogen-activated protein kinase (MAPK) signaling pathway and the calcium transduction pathway were identified in upland cotton at the seedling stage under drought stress according to annotation information and linkage disequilibrium (LD) block analysis. Moreover, RNA sequencing analysis showed that WRKY70, GhCIPK6, SnRK2.6, and NET1A were induced by drought stress, and the expression of these genes was significantly different between normal and drought stress conditions. (4) Conclusions: The present study should provide some genomic resources for drought resistance in upland cotton. Moreover, the germplasm of the different phenotypes, the detected SNPs and, the potential candidate genes will be helpful for molecular marker-assisted breeding studies about increased drought resistance in upland cotton.

Perspectives on the Application of Genome-Editing Technologies in Crop Breeding

Most conventional and modern crop-improvement methods exploit natural or artificially induced genetic variations and require laborious characterization of the progenies of multiple generations derived from time-consuming genetic crosses. Genome-editing systems, in contrast, provide the means to rapidly modify genomes in a precise and predictable way, making it possible to introduce improvements directly into elite varieties. Here, we describe the range of applications available to agricultural researchers using existing genome-editing tools. In addition to providing examples of genome-editing applications in crop breeding, we discuss the technical and social challenges faced by breeders using genome-editing tools for crop improvement.

Identification of Single Nucleotide Polymorphisms Related to the Resistance Against Acute Hepatopancreatic Necrosis Disease in the Pacific White Shrimp Litopenaeus vannamei by Target Sequencing Approach

Acute hepatopancreatic necrosis disease (AHPND) is a major bacterial disease in Pacific white shrimp Litopenaeus vannamei farming, which is caused by Vibrio parahaemolyticus. AHPND has led to a significant reduction of shrimp output since its outbreak. Selective breeding of disease-resistant broodstock is regarded as a key strategy in solving the disease problem. Understanding the relationship between genetic variance and AHPND resistance is the basis for marker-assisted selection in shrimp. The purpose of this study was to identify single nucleotide polymorphisms (SNPs) associated with the resistance against AHPND in L. vannamei. In this work, two independent populations were used for V. parahaemolyticus challenge and the resistant or susceptible shrimp were evaluated according to the survival time after Vibrio infection. The above two populations were genotyped separately by a SNP panel designed based on the target sequencing platform using a pooling strategy. The SNP panel contained 508 amplicons from DNA fragments distributed evenly along the genome and some immune-related genes of L. vannamei. By analyzing the allele frequency in the resistant and susceptible groups, 30 SNPs were found to be significantly associated with the resistance of the shrimp against V. parahaemolyticus infection (false discovery rate corrected at P < 0.05). Three SNPs were further validated by individual genotyping in all samples of population 1. Our study illustrated that target sequencing and pooling sequencing were effective in identifying the markers associated with economic traits, and the SNPs identified in this study could be used as molecular markers for breeding disease-resistant shrimp.

Natural alleles of GLA for grain length and awn development were differently domesticated in rice subspecies japonica and indica

Rice (Oryza sativa L.) cultivars harbour morphological and physiological traits different from those of wild rice (O. rufipogon Griff.), but the molecular mechanisms underlying domestication remain controversial. Here, we show that awn and long grain traits in the near-isogenic NIL-GLA are separately controlled by variations within the GLA (Grain Length and Awn Development) gene, a new allele of GAD1/RAE2, which encodes one member of the EFPL (epidermal patterning factor-like protein) family. Haplotype analyses and transgenic studies revealed that InDel1 (variation for grain length, VGL) in the promoter region of GLA (GLA^VGL ) increases grain length by promoting transcription of GLA. Absence of InDel3 (variation for awn formation, VA) in the coding region (CDS) of GLA (GLA^va ) results in short awn or no awn phenotypes. Analyses of minimum spanning trees and introgression regions demonstrated that An-1, an important gene for awn formation, was preferentially domesticated and its mutation to an-1 was followed by GLA and An-2. Gene flow then occurred between the evolved japonica and indica populations. Quality analysis showed that GLA causes poor grain quality. During genetic improvement, awnlessness was selected in ssp. indica, whereas short-grained and awnless phenotypes with good quality were selected in japonica. Our findings facilitate an understanding of rice domestication and provide a favourable allele for rice breeding.

The Maize Clade A PP2C Phosphatases Play Critical Roles in Multiple Abiotic Stress Responses

As the core components of abscisic acid (ABA) signal pathway, Clade A PP2C (PP2C-A) phosphatases in ABA-dependent stress responses have been well studied in Arabidopsis. However, the roles and natural variations of maize PP2C-A in stress responses remain largely unknown. In this study, we investigated the expression patterns of ZmPP2C-As treated with multiple stresses and generated transgenic Arabidopsis plants overexpressing most of the ZmPP2C-A genes. The results showed that the expression of most ZmPP2C-As were dramatically induced by multiple stresses (drought, salt, and ABA), indicating that these genes may have important roles in response to these stresses. Compared with wild-type plants, ZmPP2C-A1, ZmPP2C-A2, and ZmPP2C-A6 overexpression plants had higher germination rates after ABA and NaCl treatments. ZmPP2C-A2 and ZmPP2C-A6 negatively regulated drought responses as the plants overexpressing these genes had lower survival rates, higher leaf water loss rates, and lower proline accumulation compared to wild type plants. The natural variations of ZmPP2C-As associated with drought tolerance were also analyzed and favorable alleles were detected. We widely studied the roles of ZmPP2C-A genes in stress responses and the natural variations detected in these genes have the potential to be used as molecular markers in genetic improvement of maize drought tolerance.

Identification of new rice cultivars and resistance loci against rice black-streaked dwarf virus disease through genome-wide association study

BACKGROUND

The rice black-streaked dwarf virus (RBSDV) disease causes severe rice yield losses in Eastern China and other East Asian countries. Breeding resistant cultivars is the most economical and effective strategy to control the disease. However, few varieties and QTLs for RBSDV resistance have been identified to date.

RESULTS

In this study, we conducted a genome-wide association study (GWAS) on RBSDV resistance using the rice diversity panel 1 (RDP1) cultivars that were genotyped by a 44,000 high-density single nucleotide polymorphism (SNP) markers array. We found that less than 15% of these cultivars displayed resistance to RBSDV when tested under natural infection conditions at two locations with serious RBSDV occurrence. The aus, indica and tropical japonica sub-populations displayed higher RBSDV resistance than the aromatic and temperate japonica sub-populations. In particular, we identified four varieties that displayed stable levels of RBSDV resistance at all testing locations. GWAS identified 84 non-redundant SNP loci significantly associated with RBSDV resistance at two locations, leading to the identification of 13 QTLs for RBSDV resistance. Among them, qRBSDV-4.2 and qRBSDV-6.3 were detected at both locations, suggesting their resistance stability against environmental influence. Field disease evaluations showed that qRBSDV-6.3 significantly reduces RBSDV disease severity by 20%. Furthermore, introgression of qRBSDV-6.3 into two susceptible rice cultivars by marker-assisted selection demonstrated the effectiveness of qRBSDV-6.3 in enhancing RBSDV resistance.

CONCLUSIONS

The new resistant cultivars and QTLs against RBSDV disease identified in this study provide important information and genetic materials for the cloning of RBSDV resistance genes as well as developing RBSDV resistant varieties through marker-assisted selection.

Identification of new rice cultivars and resistance loci against rice black-streaked dwarf virus disease through genome-wide association study

BACKGROUND

The rice black-streaked dwarf virus (RBSDV) disease causes severe rice yield losses in Eastern China and other East Asian countries. Breeding resistant cultivars is the most economical and effective strategy to control the disease. However, few varieties and QTLs for RBSDV resistance have been identified to date.

RESULTS

In this study, we conducted a genome-wide association study (GWAS) on RBSDV resistance using the rice diversity panel 1 (RDP1) cultivars that were genotyped by a 44,000 high-density single nucleotide polymorphism (SNP) markers array. We found that less than 15% of these cultivars displayed resistance to RBSDV when tested under natural infection conditions at two locations with serious RBSDV occurrence. The aus, indica and tropical japonica sub-populations displayed higher RBSDV resistance than the aromatic and temperate japonica sub-populations. In particular, we identified four varieties that displayed stable levels of RBSDV resistance at all testing locations. GWAS identified 84 non-redundant SNP loci significantly associated with RBSDV resistance at two locations, leading to the identification of 13 QTLs for RBSDV resistance. Among them, qRBSDV-4.2 and qRBSDV-6.3 were detected at both locations, suggesting their resistance stability against environmental influence. Field disease evaluations showed that qRBSDV-6.3 significantly reduces RBSDV disease severity by 20%. Furthermore, introgression of qRBSDV-6.3 into two susceptible rice cultivars by marker-assisted selection demonstrated the effectiveness of qRBSDV-6.3 in enhancing RBSDV resistance.

CONCLUSIONS

The new resistant cultivars and QTLs against RBSDV disease identified in this study provide important information and genetic materials for the cloning of RBSDV resistance genes as well as developing RBSDV resistant varieties through marker-assisted selection.

Identification of Loci and Candidate Genes Responsible for Pod Dehiscence in Soybean via Genome-Wide Association Analysis Across Multiple Environments

Pod dehiscence (shattering) is the main cause of serious yield loss during the soybean mechanical harvesting process. A better understanding of the genetic architecture and molecular mechanisms of pod dehiscence is of great significance for soybean breeding. In this study, genome-wide association analysis (GWAS) with NJAU 355K SoySNP array was performed to detect single nucleotide polymorphisms (SNPs) associated with pod dehiscence in an association panel containing 211 accessions across five environments. A total of 163 SNPs were identified as significantly associated with pod dehiscence. Among these markers, 136 SNPs identified on chromosome 16 were located in the known QTL qPDH1. One, one, three, eleven, three, one, three, three and one SNPs were distributed on chromosome 1, 4, 6, 8, 9, 11, 17, 18, and 20, respectively. Favorable SNPs and six haplotypes were identified based on ten functional SNPs; among those Hap2 and Hap3 were considered as optimal haplotypes. In addition, based on GWAS results, the candidate gene Glyma09g06290 was identified. Quantitative real-time PCR (qRT-PCR) results and polymorphism analysis suggested that Glyma09g06290 might be involved in pod dehiscence. Furthermore, a derived cleaved amplified polymorphic sequences (dCAPS) marker for Glyma09g06290 was developed. Overall, the loci and genes identified in this study will be helpful in breeding soybean accessions resistant to pod dehiscence.

Genome-Wide Analysis of TCP Family Genes in Zea mays L. Identified a Role for ZmTCP42 in Drought Tolerance

The Teosinte-branched 1/Cycloidea/Proliferating (TCP) plant-specific transcription factors (TFs) have been demonstrated to play a fundamental role in plant development and organ patterning. However, it remains unknown whether or not the TCP gene family plays a role in conferring a tolerance to drought stress in maize, which is a major constraint to maize production. In this study, we identified 46 ZmTCP genes in the maize genome and systematically analyzed their phylogenetic relationships and synteny with rice, sorghum, and ArabidopsisTCP genes. Expression analysis of the 46 ZmTCP genes in different tissues and under drought conditions, suggests their involvement in maize response to drought stress. Importantly, genetic variations in ZmTCP32 and ZmTCP42 are significantly associated with drought tolerance at the seedling stage. RT-qPCR results suggest that ZmTCP32 and ZmTCP42 RNA levels are both induced by ABA, drought, and polyethylene glycol treatments. Based on the significant association between the genetic variation of ZmTCP42 and drought tolerance, and the inducible expression of ZmTCP42 by drought stress, we selected ZmTCP42, to investigate its function in drought response. We found that overexpression of ZmTCP42 in Arabidopsis led to a hypersensitivity to ABA in seed germination and enhanced drought tolerance, validating its function in drought tolerance. These results suggested that ZmTCP42 functions as an important TCP TF in maize, which plays a positive role in drought tolerance.

Parallelism and convergence in post-domestication adaptation in cereal grasses

The selection of desirable traits in crops during domestication has been well studied. Many crops share a suite of modified phenotypic characteristics collectively known as the domestication syndrome. In this sense, crops have convergently evolved. Previous work has demonstrated that, at least in some instances, convergence for domestication traits has been achieved through parallel molecular means. However, both demography and selection during domestication may have placed limits on evolutionary potential and reduced opportunities for convergent adaptation during post-domestication migration to new environments. Here we review current knowledge regarding trait convergence in the cereal grasses and consider whether the complexity and dynamism of cereal genomes (e.g., transposable elements, polyploidy, genome size) helped these species overcome potential limitations owing to domestication and achieve broad subsequent adaptation, in many cases through parallel means. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.

Genome-wide association study dissects the genetic bases of salt tolerance in maize seedlings

Excess salinity is a natural stress that causes crop yield losses worldwide. The genetic bases of maize salt tolerance remain largely unknown. Here we investigated the survival rates of 445 maize natural accessions after salt treatments. A skewed distribution of the salt-tolerant phenotypes was observed in this population. Genome-wide association studies (GWAS) revealed 57 loci significantly associated with salt tolerance. Forty-nine candidate genes were detected from these loci. About 10% of these genes were co-localized with loci from QTL mapping. Forty four percent of the candidate genes were involved in stress responses, ABA signaling, stomata division, DNA binding/transcription regulation and auxin signaling, suggesting that they are key genetic mechanisms of maize salt tolerance. Transgenic studies showed that two genes, the salt-tolerance-associated-gene 4 (SAG4, GRMZM2G077295) and SAG6 (GRMZM2G106056), which encode a protein transport protein and the double-strand break repair protein MRE11, respectively, had positive roles in plant salt tolerance, and their salt-tolerant haplotypes were revealed. The genes we identified in this study provide a list of candidate targets for further study of maize salt tolerance, and of genetic markers and materials that may be used for breeding salt-tolerance in maize.