Maize-Tripsacum-Teosinte allopolyploid (MTP), a novel dwarf mutant inducer tool in maize.

Dwarf plant architecture facilitates dense planting, and increased planting densities boost the maize yield. However, breeding applications of dwarfing materials for maize are currently limited. There is an urgent need remove the obstacles to applying dwarf resources. Here, we innovated a new method to add a novel maize dwarf germplasm through the distant hybridization of Maize-Tripsacum-Teosinte allopolyploid (MTP) with maize. We identified ten independent dwarf families with unique characteristics. Five germplasms in our library were controlled by their respective dwarf genes. However, no allele was controlled by Br2. Subsequently, d024 in the library was successfully fine mapped, revealing its linkage to indel-4 in ZmCYP90D1. The indel-4 polymorphism regulates the expression of ZmCYP90D1 and is controlled by an upstream transcription factor (ZmBES1/BZR1-5). The indel-4 of ZmCYP90D1 allele, which reduces plant height, originated from Tripsacum, a wild variety of maize. However, d024 exhibits sensitivity to brassinosteroids (BRs), with lower castasterone levels in the internodes than that in the wild type. Furthermore, ZmCYP90D1 interacted with ZmFDXs and ZmNAD(P)H to positively regulate the downstream BR synthesis pathway. Additionally, we showed that introgressing the indel-4 of the Tripsacum allele into modern hybrids ensures yield potential and improves the harvest index under high-density conditions. Overall, as we begin to manufacture highly engineered dwarf materials using the MTP, this approach will solve the problems faced by corn dwarfs.

Fine mapping and candidate gene analysis of qSRC3 controlling the silk color in maize (Zea mays L.).

KEY MESSAGE: Fine mapping of the maize QTL qSRC3, responsible for red silk, uncovered the candidate gene ZmMYB20, which encodes an R2R3-MYB transcription factor, has light-sensitive expression, and putatively regulates genes expression associated with anthocyanin biosynthesis. Colorless silk is a key characteristic contributing to the visual quality of fresh corn intended for market distribution. Nonetheless, the identification of Mendelian trait loci and associated genes that control silk color has been scarce. In this study, a F2 population arising from the hybridization of the single-segment substitution line qSRC3MT1 with red silk, carrying an introgressed allele from teosinte (Zea mays ssp. mexicana), and the recurrent maize inbred line Mo17, characterized by light green silk, was utilized for fine mapping. We found that the red silk trait is controlled by a semi-dominant genetic locus known as qSRC3, and its expression is susceptible to light-mediated inhibition. Moreover, qSRC3 explained 68.78% of the phenotypic variance and was delimited to a 133.2 kb region, which includes three genes. Subsequent expression analyses revealed that ZmMYB20 (Zm00001d039700), which encodes an R2R3-MYB transcription factor, was the key candidate gene within qSRC3. Yeast one-hybrid and dual-luciferase reporter assays provided evidence that ZmMYB20 suppresses the expression of two crucial anthocyanin biosynthesis genes, namely ZmF3H and ZmUFGT, by directly binding to their respective promoter regions. Our findings underscore the significance of light-inhibited ZmMYB20 in orchestrating the spatial and temporal regulation of anthocyanin biosynthesis. These results advance the production of colorless silk in fresh corn, responding to the misconception that fresh corn with withered colored silk is not fresh and providing valuable genetic resources for the improvement of sweet and waxy maize.

Genome dosage alteration caused by chromosome pyramiding and shuffling effects on karyotypic heterogeneity, reproductive diversity, and phenotypic variation in Zea-Tripsacum allopolyploids.

KEY MESSAGE: We developed an array of Zea-Tripsacum tri-hybrid allopolyploids with multiple ploidies. We unveiled that changes in genome dosage due to the chromosomes pyramiding and shuffling of three species effects karyotypic heterogeneity, reproductive diversity, and phenotypic variation in Zea-Tripsacum allopolyploids. Polyploidy, or whole genome duplication, has played a major role in evolution and speciation. The genomic consequences of polyploidy have been extensively studied in many plants; however, the extent of chromosomal variation, genome dosage, phenotypic diversity, and heterosis in allopolyploids derived from multiple species remains largely unknown. To address this question, we synthesized an allohexaploid involving Zea mays, Tripsacum dactyloides, and Z. perennis by chromosomal pyramiding. Subsequently, an allooctoploid and an allopentaploid were obtained by hybridization of the allohexaploid with Z. perennis. Moreover, we constructed three populations with different ploidy by chromosomal shuffling (allopentaploid × Z. perennis, allohexaploid × Z. perennis, and allooctoploid × Z. perennis). We have observed 3 types of sexual reproductive modes and 2 types of asexual reproduction modes in the tri-species hybrids, including 2n gamete fusion (2n + n), haploid gamete fusion (n + n), polyspermy fertilization (n + n + n) or 2n gamete fusion (n + 2n), haploid gametophyte apomixis, and asexual reproduction. The tri-hybrids library presents extremely rich karyotype heterogeneity. Chromosomal compensation appears to exist between maize and Z. perennis. A rise in the ploidy of the trihybrids was linked to a higher frequency of chromosomal translocation. Variation in the degree of phenotypic diversity observed in different segregating populations suggested that genome dosage effects phenotypic manifestation. These findings not only broaden our understanding of the mechanisms of polyploid formation and reproductive diversity but also provide a novel insight into genome pyramiding and shuffling driven genome dosage effects and phenotypic diversity.

Integrated single-molecule real-time sequencing and RNA sequencing reveal the molecular mechanisms of salt tolerance in a novel synthesized polyploid genetic bridge between maize and its wild relatives.

BACKGROUND: Tripsacum dactyloides (2n = 4x = 72) and Zea perennis (2n = 4x = 40) are tertiary gene pools of Zea mays L. and exhibit many abiotic adaptations absent in modern maize, especially salt tolerance. A previously reported allopolyploid (hereafter referred to as MTP, 2n = 74) synthesized using Zea mays, Tripsacum dactyloides, and Zea perennis has even stronger salt tolerance than Z. perennis and T. dactyloides. This allopolyploid will be a powerful genetic bridge for the genetic improvement of maize. However, the molecular mechanisms underlying its salt tolerance, as well as the key genes involved in regulating its salt tolerance, remain unclear. RESULTS: Single-molecule real-time sequencing and RNA sequencing were used to identify the genes involved in salt tolerance and reveal the underlying molecular mechanisms. Based on the SMRT-seq results, we obtained 227,375 reference unigenes with an average length of 2300 bp; most of the unigenes were annotated to Z. mays sequences (76.5%) in the NR database. Moreover, a total of 484 and 1053 differentially expressed genes (DEGs) were identified in the leaves and roots, respectively. Functional enrichment analysis of DEGs revealed that multiple pathways responded to salt stress, including "Flavonoid biosynthesis," "Oxidoreductase activity," and "Plant hormone signal transduction" in the leaves and roots, and "Iron ion binding," "Acetyl-CoA carboxylase activity," and "Serine-type carboxypeptidase activity" in the roots. Transcription factors, such as those in the WRKY, B3-ARF, and bHLH families, and cytokinin negatively regulators negatively regulated the salt stress response. According to the results of the short time series-expression miner analysis, proteins involved in "Spliceosome" and "MAPK signal pathway" dynamically responded to salt stress as salinity changed. Protein-protein interaction analysis revealed that heat shock proteins play a role in the large interaction network regulating salt tolerance. CONCLUSIONS: Our results reveal the molecular mechanism underlying the regulation of MTP in the response to salt stress and abundant salt-tolerance-related unigenes. These findings will aid the retrieval of lost alleles in modern maize and provide a new approach for using T. dactyloides and Z. perennis to improve maize.

Fine mapping and candidate gene analysis of a novel fertility restorer gene for C-type cytoplasmic male sterility in maize (Zea mays L.).

KEY MESSAGE: A novel strong fertility restorer gene Rf12 for C-type cytoplasmic male sterility of maize was finely mapped on chromosome 2. Its best candidate gene Zm00001d007531 is predicted to encode a p-type PPR protein. The lack of strong restorer gene of maize CMS-C greatly limits its application in hybrid seed production. Therefore, the cloning of maize CMS-C novel strong restorer genes is necessary. In this study, a strong restorer line ZH91 for maize CMS-C was found, and the novel restorer gene named Rf12 in ZH91 had been mapped in a 146 kb physical interval on maize chromosome 2. Using the third-generation high-throughput sequencing (ONT), the whole genome sequence of ZH91 was got, and with integrating the annotation information of the reference genome B73_RefGen_v4 and B73_RefGen_v5, four candidate genes were predicted in ZH91 within the mapping region. Then using gene cloning, stranded specific RNA sequencing, qRT-PCR analysis and subcellular localization, Zm00001d007531 was identified as the most likely candidate gene of Rf12. Zm00001d007531 encodes a p-type PPR protein with 19 PPR motifs and targets mitochondria and chloroplast. Stranded specific RNA sequencing and qRT-PCR results both show that the expression of Zm00001d007531 between anthers of near-isogenic lines C478Rf12Rf12 and C478rf12rf12 was significantly difference in pollen mother cell stage. And the result of sequence alignment for Zm00001d007531 gene in 60 materials showed that there are twelve SNPs in CDS region of Zm00001d007531 were tightly linked to the fertility. The finding of a novel strong restorer germplasm resource ZH91 for maize CMS-C can greatly promote the application of maize CMS-C line in maize hybrid seeds production, and the identification of candidate gene Zm00001d007531 can accelerate the backcrossing process of maize CMS-C strong restorer gene Rf12 to some extent.

QTL-seq and transcriptomic integrative analyses reveal two positively regulated genes that control the low-temperature germination ability of MTP-maize introgression lines.

KEY MESSAGE: Two candidate genes (ZmbZIP113 and ZmTSAH1) controlling low-temperature germination ability were identified by QTL-seq and integrative transcriptomic analyses. The functional verification results showed that two candidate genes positively regulated the low-temperature germination ability of IB030. Low-temperature conditions cause slow maize (Zea mays L.) seed metabolism, resulting in slow seedling emergence and irregular seedling emergence, which can cause serious yield loss. Thus, improving a maize cultivar's low-temperature germination ability (LTGA) is vital for increasing yield production. Wild relatives of maize, such as Z. perennis and Tripsacum dactyloides, are strongly tolerant of cold stress and can thus be used to improve the LTGA of maize. In a previous study, the genetic bridge MTP was constructed (from maize, T. dactyloides, and Z. perennis) and used to obtain a highly LTGA maize introgression line (IB030) by backcross breeding. In this study, IB030 (Strong-LTGA) and Mo17 (Weak-LTGA) were selected as parents to construct an F2 offspring. Additionally, two major QTLs (qCS1-1 and qCS10-1) were mapped. Then, RNA-seq was performed using seeds of IB030 and the recurrent parent B73 treated at 10 °C for 27 days and 25 °C for 7 days, respectively, and two candidate genes (ZmbZIP113 and ZmTSAH1) controlling LTGA were located using QTL-seq and integrative transcriptomic analyses. The functional verification results showed that the two candidate genes positively regulated LTGA of IB030. Notably, homologous cloning showed that the source of variation in both candidate genes was the stable inheritance of introgressed alleles from Z. perennis. This study was thus able to analyze the LTGA mechanism of IB030 and identify resistance genes for genetic improvement in maize, and it proved that using MTP genetic bridge confers desirable traits or phenotypes of Z. perennis and tripsacum essential to maize breeding systems.

Deploying QTL-seq rapid identification and separation of the major QTLs of tassel branch number for fine-mapping in advanced maize populations.

The tassel competes with the ear for nutrients and shields the upper leaves, thereby reducing the yield of grain. The tassel branch number (TBN) is a pivotal determinant of tassel size, wherein the reduced TBN has the potential to enhance the transmission of light and reduce the consumption of nutrients, which should ultimately result in increased yield. Consequently, the TBN has emerged as a vital target trait in contemporary breeding programs that focus on compact maize varieties. In this study, QTL-seq technology and advanced population mapping were used to rapidly identify and dissect the major effects of the TBN on QTL. Advanced mapping populations (BC4F2 and BC4F3) were derived from the inbred lines 18-599 (8-11 TBN) and 3237 (0-1 TBN) through phenotypic recurrent selection. First, 13 genomic regions associated with the TBN were detected using quantitative trait locus (QTL)-seq and were located on chromosomes 2 and 5. Subsequently, validated loci within these regions were identified by QTL-seq. Three QTLs for TBN were identified in the BC4F2 populations by traditional QTL mapping, with each QTL explaining the phenotypic variation of 6.13-18.17%. In addition, for the major QTL (qTBN2-2 and qTBN5-1), residual heterozygous lines (RHLs) were developed from the BC4F2 population. These two major QTLs were verified in the RHLs by QTL mapping, with the phenotypic variation explained (PVE) of 21.57% and 30.75%, respectively. Near-isogenic lines (NILs) of qTBN2-2 and qTBN5-1 were constructed. There were significant differences between the NILs in TBN. These results will enhance our understanding of the genetic basis of TBN and provide a solid foundation for the fine-mapping of TBN. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-023-01431-y.

QTL Mapping and a Transcriptome Integrative Analysis Uncover the Candidate Genes That Control the Cold Tolerance of Maize Introgression Lines at the Seedling Stage.

Chilling injury owing to low temperatures severely affects the growth and development of maize (Zea mays.L) seedlings during the early and late spring seasons. The existing maize germplasm is deficient in the resources required to improve maize's ability to tolerate cold injury. Therefore, it is crucial to introduce and identify excellent gene/QTLs that confer cold tolerance to maize for sustainable crop production. Wild relatives of maize, such as Z. perennis and Tripsacum dactyloides, are strongly tolerant to cold and can be used to improve the cold tolerance of maize. In a previous study, a genetic bridge among maize that utilized Z. perennis and T. dactyloides was created and used to obtain a highly cold-tolerant maize introgression line (MIL)-IB030 by backcross breeding. In this study, two candidate genes that control relative electrical conductivity were located on MIL-IB030 by forward genetics combined with a weighted gene co-expression network analysis. The results of the phenotypic, genotypic, gene expression, and functional verification suggest that two candidate genes positively regulate cold tolerance in MIL-IB030 and could be used to improve the cold tolerance of cultivated maize. This study provides a workable route to introduce and mine excellent genes/QTLs to improve the cold tolerance of maize and also lays a theoretical and practical foundation to improve cultivated maize against low-temperature stress.

Identification of a major QTL and genome-wide epistatic interactions for single vs. paired spikelets in a maize-teosinte F2 population.

Maize ear carries paired spikelets, whereas the ear of its wild ancestor, teosinte, bears single spikelets. However, little is known about the genetic basis of the processes of transformation of single spikelets in teosinte ear to paired spikelets in maize ear. In this study, a two-ranked, paired-spikelets primitive maize and a two-ranked, single-spikelet teosinte were utilized to develop an F2 population, and quantitative trait locus (loci) (QTL) mapping for single vs. paired spikelets (PEDS) was performed. One major QTL (qPEDS3.1) for PEDS located on chromosome 3S was identified in the 162 F2 plants using the inclusive composite interval mapping of additive (ICIM-ADD) module, explaining 23.79% of the phenotypic variance. Out of the 409 F2 plants, 43 plants with PEDS = 0% and 43 plants with PEDS > 20% were selected for selective genotyping, and the QTL (qPEDS3.1) was detected again. Moreover, the QTL (qPEDS3.1) was validated in three environments, which explained 31.05%, 38.94%, and 23.16% of the phenotypic variance, respectively. In addition, 50 epistatic QTLs were detected in the 162 F2 plants using the two-locus epistatic QTL (ICIM-EPI) module; they were distributed on all 10 chromosomes and explained 94.40% of the total phenotypic variance. The results contribute to a better understanding of the genetic basis of domestication of paired spikelets and provide a genetic resource for future map-based cloning; in addition, the systematic dissection of epistatic interactions underlies a theoretical framework for overcoming epistatic effects on QTL fine mapping. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-022-01276-x.

Combining QTL-seq and linkage mapping to uncover the genetic basis of single vs. paired spikelets in the advanced populations of two-ranked maize×teosinte.

BACKGROUND: Teosinte ear bears single spikelet, whereas maize ear bears paired spikelets, doubling the number of grains in each cupulate during maize domestication. In the past 20 years, genetic analysis of single vs. paired spikelets (PEDS) has been stagnant. A better understanding of genetic basis of PEDS could help fine mapping of quantitative trait loci (QTL) and cloning of genes. RESULTS: In this study, the advanced mapping populations (BC3F2 and BC4F2) of maize × teosinte were developed by phenotypic recurrent selection. Four genomic regions associated with PEDS were detected using QTL-seq, located on 194.64-299.52 Mb, 0-162.80 Mb, 12.82-97.17 Mb, and 125.06-157.01 Mb of chromosomes 1, 3, 6, and 8, respectively. Five QTL for PEDS were identified in the regions of QTL-seq using traditional QTL mapping. Each QTL explained 1.12-38.05% of the phenotypic variance (PVE); notably, QTL qPEDS3.1 with the average PVE of 35.29% was identified in all tests. Moreover, 14 epistatic QTL were detected, with the total PVE of 47.57-66.81% in each test. The QTL qPEDS3.1 overlapped with, or was close to, one locus of 7 epistatic QTL. Near-isogenic lines (NILs) of QTL qPEDS1.1, qPEDS3.1, qPEDS6.1, and qPEDS8.1 were constructed. All individuals of NIL-qPEDS6.1(MT1) and NIL-qPEDS8.1(MT1) showed paired spikelets (PEDS = 0), but the flowering time was 7 days shorter in the NIL-qPEDS8.1(MT1). The ratio of plants with PEDS > 0 was low (1/18 to 3/18) in the NIL-qPEDS1.1(MT1) and NIL-qPEDS3.1(MT1), maybe due to the epistatic effect. CONCLUSION: Our results suggested that major QTL, minor QTL, epistasis and photoperiod were associated with the variation of PEDS, which help us better understand the genetic basis of PEDS and provide a genetic resource for fine mapping of QTL.

Metabolite profiling and genome-wide association studies reveal response mechanisms of phosphorus deficiency in maize seedling.

Inorganic phosphorus (Pi) is an essential element in numerous metabolic reactions and signaling pathways, but the molecular details of these pathways remain largely unknown. In this study, metabolite profiles of maize (Zea mays L.) leaves and roots were compared between six low-Pi-sensitive lines and six low-Pi-tolerant lines under Pi-sufficient and Pi-deficient conditions to identify pathways and genes associated with the low-Pi stress response. Results showed that under Pi deprivation the concentrations of nucleic acids, organic acids and sugars were increased, but that the concentrations of phosphorylated metabolites, certain amino acids, lipid metabolites and nitrogenous compounds were decreased. The levels of secondary metabolites involved in plant immune reactions, including benzoxazinoids and flavonoids, were significantly different in plants grown under Pi-deficient conditions. Among them, the 11 most stable metabolites showed significant differences under low- and normal-Pi conditions based on the coefficient of variation (CV). Isoleucine and alanine were the most stable metabolites for the identification of Pi-sensitive and Pi-resistant maize inbred lines. With the significant correlation between morphological traits and metabolites, five low-Pi-responding consensus genes associated with morphological traits and simultaneously involved in metabolic pathways were mined by combining metabolites profiles and genome-wide association study (GWAS). The consensus genes induced by Pi deficiency in maize seedlings were also validated by reverse-transcription quantitative polymerase chain reaction (RT-qPCR). Moreover, these genes were further validated in a recombinant inbred line (RIL) population, in which the glucose-6-phosphate-1-epimerase encoding gene mediated yield and correlated traits to phosphorus availability. Together, our results provide a framework for understanding the metabolic processes underlying Pi-deficient responses and give multiple insights into improving the efficiency of Pi use in maize.

Analysis of the genitor origin of an intergeneric hybrid clone between Zea and Tripsacum for forage production by McGISH.

In this study, the chromosome number and composition of a novel perennial forage crop, 'Yucao No. 6' (Yu6), was revealed by chromosome spread and McGISH (multicolor genomic in situ hybridization) techniques to clarify its genitor origin. Cytogenetic analysis showed that Yu6, which has 56 chromosomes, is an aneuploid representing 12, 17 and 27 chromosomes from Zea mays ssp. mays L. (Zm, 2n = 2x = 20), Tripsacum dactyloides L. (Td, 2n = 4x = 72), and Z. perennis (Hitchc.) Reeves & Mangelsd. (Zp, 2n = 4x = 40), respectively. This finding indicates that Yu6 is the product of a reduced egg (n = 36 = 12Zm + 17Td + 7Zp) of MTP (a near-allohexaploid hybrid, 2n = 74 = 20Zm + 34Td + 20Zp) fertilized by a haploid sperm nucleus (n = 20Zp) of Z. perennis. Moreover, 3 translocated chromosomes consisting of the maize-genome chromosome with the segment of Z. perennis were observed. These results suggest that it is practical to develop perennial forage maize by remodeling the chromosomal architecture of MTP offspring with Z. perennis as a pollen parent. Finally, the overview of forage breeding in the Zea and Tripsacum genera was discussed.

Genetic dissection of stalk lodging-related traits using an IBM Syn10 DH population in maize across three environments (Zea mays L.).

Stalk lodging severely limits the grain yield of maize (Zea mays L.). Mechanical stalk strength can be reflected by the traits of stalk diameter (SD), stalk bending strength (SBS), and lodging rind penetrometer resistance (RPR). To determine the genetic basis of maize stalk lodging, quantitative trait loci (QTLs) were mapped for these three traits using the IBM Syn10 DH population in three environments. The results indicated that there were strong genetic correlations among the three traits, and the analyses of phenotypic variations for SD, SBS, and RPR across the three environments showed high broad-sense heritability (0.6843, 0.5175, and 0.7379, respectively). In total, 44 significant QTLs were identified control the above traits across the 3 environments. A total of 14, 14, and 16 QTLs were identified for SD, SBS, and RPR across single-environment mapping, respectively. Notably, ten QTLs were stably expressed across multiple-environments, including two QTLs for SD, three for SBS, and five for RPR. Three major QTLs each accounting for over 10% of the phenotypic variation were qSD6-2 (10.03%), qSD8-2 (13.73%), and qSBS1-2 (11.89%). Comprehensive analysis of all QTLs in this study revealed that 5 QTL clusters including 12 QTLs were located on chromosomes 1, 3, 7, and 8, respectively. Among these 44 QTLs, 9 harbored 13 stalk lodging-associated SNPs that were detected by our recently published work, with 1 SNP successfully validated in the IBM Syn10 DH population. These chromosomal regions will be useful for marker-assisted selection and fine mapping of stalk lodging-related traits in maize.

Allopolyploidization facilitates gene flow and speciation among corn, Zea perennis and Tripsacum dactyloides.

MAIN CONCLUSION: Tripsacum dactyloides is closely related to Zea mays since Zea perennis and the MTP tri- species hybrid have four possible reproductive modes. Eastern gamagrass (Tripsacum dactyloides L.) and tetraploid perennial teosinte (Zea perennis) are well known to possess genes conferring resistance against biotic and abiotic stresses as well as adaptation to flood and aluminum toxic soils. However, plant breeders have been hampered to utilize these and other beneficial traits for maize improvement due to sterility in their hybrids. By crossing a tetraploid maize-inbred line × T. dactyloides, a female fertile hybrid was produced that was crossed with Z. perennis to yield a tri-genomic female fertile hybrid, which was backcrossed with diploid maize to produce BC1 and BC2. The tri-genomic hybrid provided a new way to transfer genetic material from both species into maize by utilizing conventional plant breeding methods. On the basis of cytogenetic observations using multi-color genomic in situ hybridization, the progenies were classified into four groups, in which chromosomes could be scaled both up and down with ease to produce material for varying breeding and genetic purposes via apomixis or sexual reproduction. In the present study, pathways were found to recover maize and to obtain specific translocations as well as a speedy recovery of the T. dactyloides-maize addition line in a second backcross generation. However, phenotypes of the recovered maize were in most cases far from maize as a result of genetic load from T. dactyloides and Z. perennis, and could not be directly used as a maize-inbred line but could serve as an intermediate material for maize improvement. A series of hybrids was produced (having varying chromosome number, constitution, and translocations) with agronomic traits from all three parental species. The present study provides an application of overcoming the initial interspecific barriers among these species. Moreover, T. dactyloides is closely related to Z. mays L. ssp. mays since Z. perennis and the MTP tri- species hybrid have four possible reproductive modes.

Natural antisense transcripts are significantly involved in regulation of drought stress in maize.

Natural antisense transcripts (NATs) are a prominent and complex class of regulatory RNAs. Using strand-specific RNA sequencing, we identified 1769 sense and antisense transcript pairs (NAT pairs) in two maize inbreds with different sensitivity to drought, as well as in two derivative recombination inbred lines (RILs). A significantly higher proportion of NATs relative to non-NATs are specifically expressed under water stress (WS). Surprisingly, expression of sense and antisense transcripts produced by NAT pairs is significantly correlated, particularly under WS. We found an unexpected large proportion of NATs with protein coding potential, as estimated by ribosome release scores. Small RNAs significantly accumulate within NAT pairs, with 21 nt smRNA particularly enriched in overlapping regions of these pairs of genes. The abundance of these smRNAs is significantly altered in the leafbladeless1 mutant, suggesting that these genes may be regulated by the tasiRNA pathway. Further, NATs are significantly hypomethylated and include fewer transposable element sequences relative to non-NAT genes. NAT gene regions also exhibit higher levels of H3K36me3, H3K9ac, and H3K4me3, but lower levels of H3K27me3, indicating that NAT gene pairs generally exhibit an open chromatin configuration. Finally, NAT pairs in 368 diverse maize inbreds and 19 segregating populations were specifically enriched for polymorphisms associated with drought tolerance. Taken together, the data highlight the potential impact of that small RNAs and histone modifications have in regulation of NAT expression, and the significance of NATs in response to WS.

Genome-wide characterization of non-reference transposable element insertion polymorphisms reveals genetic diversity in tropical and temperate maize.

BACKGROUND: Maize was originally domesticated in a tropical environment but is now widely cultivated at temperate latitudes. Temperate and tropical maize populations have diverged both genotypically and phenotypically. Tropical maize lines grown in temperate environments usually exhibit delayed flowering, pollination, and seed set, which reduces their grain yield relative to temperate adapted maize lines. One potential mechanism by which temperate maize may have adapted to a new environment is novel transposable element insertions, which can influence gene regulation. Recent advances in sequencing technology have made it possible to study variation in transposon content and insertion location in large sets of maize lines. RESULTS: In total, 274,408 non-redundant TEs (NRTEs) were identified using resequencing data generated from 83 maize inbred lines. The locations of DNA TEs and copia-superfamily retrotransposons showed significant positive correlations with gene density and genetic recombination rates, whereas gypsy-superfamily retrotransposons showed a negative correlation with these two parameters. Compared to tropical maize, temperate maize had fewer unique NRTEs but higher insertion frequency, lower background recombination rates, and higher linkage disequilibrium, with more NRTEs close to flowering and stress-related genes in the genome. Association mapping demonstrated that the presence/absence of 48 NRTEs was associated with flowering time and that expression of neighboring genes differed between haplotypes where a NRTE was present or absent. CONCLUSIONS: This study suggests that NRTEs may have played an important role in creating the variation in gene regulation that enabled the rapid adaptation of maize to diverse environments.

Identification, and Functional and Expression Analyses of the CorA/MRS2/MGT-Type Magnesium Transporter Family in Maize.

Magnesium (Mg(2+)) is an essential macronutrient for plant growth and development, and the CorA/MRS2/MGT-type Mg(2+) transporters play important roles in maintaining Mg(2+) homeostasis in plants. Although the MRS2/MGT genes have been identified in two model plant species, Arabidopsis and rice, a comprehensive analysis of the MRS2/MGT gene family in other plants is lacking. In this work, 12 putative MRS2/MGT genes (ZmMGT1- ZmMGT12) were identified in maize and all of them were classified into five distinct subfamilies by phylogenetic analysis. A complementation assay in the Salmonella typhimurium MM281 strain showed that five representatives of the 12 members possess Mg(2+) transport abilities. Inhibition of ZmMGT protein activity using the hexaamminecobalt (III) (Co-Hex) inhibitor indicated that the ZmMGT protein mediated both low-affinity and high-affinity Mg(2+) transport in maize. A semi-quantitative reverse transcription-PCR (RT-PCR) analysis revealed that eight genes were constitutively expressed in all of the detected tissues, with one being specifically expressed in roots and three having no detectable expression signals. A quantitative RT-PCR analysis showed that some ZmMGT members displayed differential responses to Mg(2+) deficiency and aluminum (Al) stress. Furthermore, root growth inhibition and Mg(2+) accumulation analyses in two maize inbred lines, which conferred different levels of Al tolerance, revealed that ZmMGT proteins contributed to the Al resistance of the Al tolerance genotype. We hypothesize that ZmMGT family members function as Mg(2+) transporters and may play a role in linking Mg(2+) deficiency and Al stress responses. Our results will be valuable in a further analysis of the important biological functions of ZmMGT members in maize.

Development of genome-wide insertion and deletion markers for maize, based on next-generation sequencing data.

BACKGROUND: Insertions and deletions (indels) are the most abundant form of structural variation in all genomes. Indels have been increasingly recognized as an important source of molecular markers due to high-density occurrence, cost-effectiveness, and ease of genotyping. Coupled with developments in bioinformatics, next-generation sequencing (NGS) platforms enable the discovery of millions of indel polymorphisms by comparing the whole genome sequences of individuals within a species. RESULTS: A total of 1,973,746 unique indels were identified in 345 maize genomes, with an overall density of 958.79 indels/Mbp, and an average allele number of 2.76, ranging from 2 to 107. There were 264,214 indels with polymorphism information content (PIC) values greater than or equal to 0.5, accounting for 13.39% of overall indels. Of these highly polymorphic indels, we designed primer pairs for 83,481 and 29,403 indels with major allele differences (i.e. the size difference between the most and second most frequent alleles) greater than or equal to 3 and 8 bp, respectively, based on the differing resolution capabilities of gel electrophoresis. The accuracy of our indel markers was experimentally validated, and among 100 indel markers, average accuracy was approximately 90%. In addition, we also validated the polymorphism of the indel markers. Of 100 highly polymorphic indel markers, all had polymorphisms with average PIC values of 0.54. CONCLUSIONS: The maize genome is rich in indel polymorphisms. Intriguingly, the level of polymorphism in genic regions of the maize genome was higher than that in intergenic regions. The polymorphic indel markers developed from this study may enhance the efficiency of genetic research and marker-assisted breeding in maize.

Identification of candidate genes for drought tolerance by whole-genome resequencing in maize.

BACKGROUND: Drought stress is one of the major limiting factors for maize production. With the availability of maize B73 reference genome and whole-genome resequencing of 15 maize inbreds, common variants (CV) and clustering analyses were applied to identify non-synonymous SNPs (nsSNPs) and corresponding candidate genes for drought tolerance. RESULTS: A total of 524 nsSNPs that were associated with 271 candidate genes involved in plant hormone regulation, carbohydrate and sugar metabolism, signaling molecules regulation, redox reaction and acclimation of photosynthesis to environment were detected by CV and cluster analyses. Most of the nsSNPs identified were clustered in bin 1.07 region that harbored six previously reported QTL with relatively high phenotypic variation explained for drought tolerance. Genes Ontology (GO) analysis of candidate genes revealed that there were 35 GO terms related to biotic stimulus and membrane-bounded organelle, showing significant differences between the candidate genes and the reference B73 background. Changes of expression level in these candidate genes for drought tolerance were detected using RNA sequencing for fertilized ovary, basal leaf meristem tissue and roots collected under drought stressed and well-watered conditions. The results indicated that 70% of candidate genes showed significantly expression changes under two water treatments and our strategies for mining candidate genes are feasible and relatively efficient. CONCLUSIONS: Our results successfully revealed candidate nsSNPs and associated genes for drought tolerance by comparative sequence analysis of 16 maize inbred lines. Both methods we applied were proved to be efficient for identifying candidate genes for complex traits through the next-generation sequencing technologies (NGS). These selected genes will not only facilitate understanding of genetic basis of drought stress response, but also accelerate genetic improvement through marker-assisted selection in maize.

A luciferase-based method for assay of 5'-adenylylsulfate reductase.

A luciferase-based method was developed for measurement of 5'-adenylylsulfate (APS) reductase (APR), an enzyme of the reductive sulfate assimilation pathway in prokaryotes and plants. APR catalyzes the two-electron reduction of APS and forms sulfite and adenosine 5'-monophospahate (AMP). The luciferase-based assay measures AMP production using an enzyme-coupled system that generates luminescence. The method is shown to provide an accurate measurement of APR kinetic properties and can be used for both endpoint and continuous assays. APR activity can be measured from pure enzyme preparations as well as from crude protein extracts of tissues. In addition, the assay is ideally suited to high-throughput sample analysis of APR activity in a microtiter dish format. The method adds new capability to the study of the biochemistry and physiology of APR.