[Show abstract][Hide abstract] ABSTRACT: NAC (NAM, ATAF1/2 and CUC2) has been verified to regulate biological responses in various biotic and abiotic stress-resistant activities. In Zea mays, 190 NAC proteins downloaded from the Plant transcription factor (TF) database website were identified and given their unified names here. Of them, 177 maize NAC proteins that showed at least two conserved subdomains of NAC TF were used for phylogenetic analysis. The NAC proteins were compared to 18 known functional NAC TFs in Arabidopsis and rice and a total of 195 NAC proteins were phylogenetically classified into five groups. The NAC-IV group was predicted to be a SNAC (stress-responsive NAC) subfamily. For them, 13 SNAC transcripts in the SNAC subfamily showed a response to drought stress and nearly all of these transcripts in the roots under drought stress and eleven transcripts in the leaves under 12 h of drought stress were up-regulated. Most important, ZmNAC010312, ZmNAC080308 and ZmNAC030295 of SNAC subfamily were further validated to be drought-responsive candidate genes by differential expression analysis. These findings are important for drought-responsive candidate gene selection in all maize NAC genes and advances in the functional analysis of the NAC family in Zea mays.
[Show abstract][Hide abstract] ABSTRACT: Characterization of the genetic properties of maize inbred lines is beneficial not only for increasing knowledge of genetic diversity, but also for maize breeding. In the present study, a panel of 240 maize inbred lines commonly used in China, including three foundation parents Dan340, Mo17, and Huangzao4, and their derivatives, was genotyped using the MaizeSNP50 BeadChip, which contains 56,110 single-nucleotide polymorphism (SNP) markers. As a result, 40,757 SNPs with unique physical positions were successfully recalled in this panel with an average coverage of 50 kb per SNP. Five subgroups including Lan, LRC, PB, Reid, and SPT were inferred using 4000 SNPs with minor allele frequency ≥0.200, a result that was largely consistent with the pedigree information for these 240 inbred lines. With a cutoff value of r
2 < 0.100, linkage disequilibrium (LD) decay distances along the ten chromosomes of maize ranged from 397 to 819 kb, with an average of 643 kb. A subtotal of 26, 35, and 23 identity-by-descent segments, which were longer than both the average LD decay distance on the corresponding chromosomes and the local LD decay distance of r
2 < 0.100, were identified in the Dan340, Huangzao4, and Mo17 derivatives, respectively. Three lower peaks for Tajima’s D overlapped with three major quantitative trait loci (qkrn7, scmv1, and qHS2.09) in these derivatives. Elucidating the genetic properties of this panel provides information for investigating the genetic architecture of agronomic traits and heterotic grouping during maize breeding.
[Show abstract][Hide abstract] ABSTRACT: Rice black-streaked dwarf virus (RBSDV) causes maize rough dwarf disease or rice black-streaked dwarf disease and can lead to severe yield losses in maize and rice. To analyse RBSDV evolution, codon usage bias and genetic structure were investigated in 111 maize and rice RBSDV isolates from eight geographic locations in 2013 and 2014. The linear dsRNA S7 is A+U rich, with overall codon usage biased toward codons ending with A (A3s, S7-1: 32.64%, S7-2: 29.95%) or U (U3s, S7-1: 44.18%, S7-2: 46.06%). Effective number of codons (Nc) values of 45.63 in S7-1 (the first open reading frame of S7) and 39.96 in S7-2 (the second open reading frame of S7) indicate low degrees of RBSDV-S7 codon usage bias, likely driven by mutational bias regardless of year, host, or geographical origin. Twelve optimal codons were detected in S7. The nucleotide diversity (π) of S7 sequences in 2013 isolates (0.0307) was significantly higher than in 2014 isolates (0.0244, P = 0.0226). The nucleotide diversity (π) of S7 sequences in isolates from Jinan (0.0391) was higher than that from the other seven locations (P < 0.01). Only one S7 recombinant was detected in Baoding. RBSDV isolates could be phylogenetically classified into two groups according to S7 sequences, and further classified into two subgroups. S7-1 and S7-2 were under negative and purifying selection, with respective Ka/Ks ratios of 0.0179 and 0.0537. These RBSDV populations were expanding (P < 0.01) as indicated by negative values for Tajima's D, Fu and Li's D, and Fu and Li's F. Genetic differentiation was detected in six RBSDV subpopulations (P < 0.05). Absolute Fst (0.0790) and Nm (65.12) between 2013 and 2014, absolute Fst (0.1720) and Nm (38.49) between maize and rice, and absolute Fst values of 0.0085-0.3069 and Nm values of 0.56-29.61 among these eight geographic locations revealed frequent gene flow between subpopulations. Gene flow between 2013 and 2014 was the most frequent.
[Show abstract][Hide abstract] ABSTRACT: Drought is recognized as the major abiotic constraint to global food production. Molecular markers have become an important genetic tool for understanding genome dynamics and facilitating molecular breeding of drought resistance. Here, cleaved amplified polymorphic sequence (CAPS) markers dhnC397 and rspC1090 were identified based on the SNP A/G polymorphisms in the drought-resistance genes dhn1 and rsp41. The two alleles of both genes were easily and rapidly discriminated by polyacrylamide gel electrophoresis to reveal single nucleotide polymorphisms (SNPs) as functional markers. By validation of an integrated selection criterion for drought resistance, the average SI (selection index for drought resistance) of lines with superior drought-resistance genotypes was higher than those with opposite, less drought-resistant genotypes, and the SI of heterotic group B was higher than that of heterotic group A for both genes. Integrating the results of CAPS analysis and evaluation of drought resistance indicated that the SNPs in these two genes partly participate in conferring drought resistance in these maize lines of interest. Breeders can thus use the CAPS markers identified here as functional markers for the improvement of drought resistance in these maize lines and possibly others.
No preview · Article · Jan 2015 · Molecular Breeding
[Show abstract][Hide abstract] ABSTRACT: Foliar diseases are common in most maize-producing regions and have caused serious yield reduction in China. To evaluate genetic resistance of parental lines actively used in maize breeding programs to major foliar diseases, 152 maize inbred lines were tested against northern corn leaf blight (NCLB), southern corn leaf blight (SCLB), Curvularia leaf spot (CLS), gray leaf spot (GLS), common rust, and southern rust from 2003 to 2005. A small number of lines exhibited highly resistant reactions to common rust and southern rust, but none were highly resistant to NCLB, SCLB, CLS, and GLS. Although 53.3%, 40.8%, and 80.7% of lines were resistant to NCLB, SCLB, and common rust, the resistance in most lines was moderate. Resistance to CLS, GLS, and southern rust were rare in this collection of maize lines. Five lines, 313, Chang 7-2, Qi 319, Qi 318, and Shen 137, were resistant to all diseases tested. Lines belonging to heterotic subgroup PB exhibited better resistance to the foliar diseases than lines from other heterotic subgroups, such as BSSS, PA, Lancaster, LRC, and PA. The results will be of benefit to breeders for selecting lines in disease resistance breeding programs.
[Show abstract][Hide abstract] ABSTRACT: Maize rough dwarf disease (MRDD), caused by the Maize rough dwarf virus (MRDV) is highly prevalent across summer at maize-growing areas in China. To investigate the genetic architecture underlying this viral disease, a set of 236 Chinese maize inbred lines was evaluated for resistance to MRDD in 2010 and 2011. Based on 41,101 single-nucleotide polymorphism (SNP) markers with minor allele frequencies (MAF) greater than 5 %, a genome-wide association study (GWAS) was employed to identify genomic loci for resistance to MRDD. A total of 73 SNPs were found to be associated with resistance to MRDD at a significance threshold of -log10 (P) > 4 controlling the false discovery rate (FDR) at α = 0.1. Fourteen of these SNPs were detected in both of the two environments tested. A total of 48 SNPs were identified in linkage disequilibrium (LD) blocks containing candidate resistance genes, including protein kinase genes. Using the pedigree information and whole-genome SNP analysis of five highly resistant inbred lines derived from the hybrid ‘P78599’, nine derivative fragments harbouring SNPs associated with MRDD resistance were detected. One 81.57 Mb fragment in particular located in bin 8.03, which contained six SNPs associated with MRDD resistance, and included the major quantitative trait loci (QTL) that had been identified in the previous study. These results suggest that the SNPs and fragments associated with MRDD resistance, especially those in bin 8.03, could be used for fine mapping of resistance genes and developing resistant varieties in maize.
Full-text · Article · May 2014 · European Journal of Plant Pathology
[Show abstract][Hide abstract] ABSTRACT: Gray leaf spot (GLS), caused by Cercospora zeae-maydis, is an important foliar disease of maize (Zea mays L.) worldwide, resistance to which is controlled by multiple quantitative trait loci (QTL). To gain insights into the genetic architecture underlying the resistance to this disease, an association mapping population consisting of 161 inbred lines was evaluated for resistance to GLS in a plant pathology nursery at Shenyang in 2010 and 2011. Subsequently, a genome-wide association study, using 41,101 single-nucleotide polymorphisms (SNPs), identified 51 SNPs significantly (P < 0.001) associated with GLS resistance, which could be converted into 31 QTL. In addition, three candidate genes related to plant defense were identified, including nucleotide-binding-site/leucine-rich repeat, receptor-like kinase genes similar to those involved in basal defense. Two genic SNPs, PZE-103142893 and PZE-109119001, associated with GLS resistance in chromosome bins 3.07 and 9.07, can be used for marker-assisted selection (MAS) of GLS resistance. These results provide an important resource for developing molecular markers closely linked with the target trait, enhancing breeding efficiency.
[Show abstract][Hide abstract] ABSTRACT: The recessive opaque-2 mutant gene (o2) reduces α-zeins accumulation in maize endosperm, changes the amino acid composition of maize kernels, induces an opaque endosperm, and increases the lysine content of kernels. The quality protein maize (QPM) inbred line CA339 (o2o2) and an elite normal inbred line liao2345 (O2O2) were used to construct o2 near-isogenic lines (NILs) by marker-assisted selection (MAS) using the co-dominant SSR marker phi057. Two specific o2 NILs were constructed, named liao2345/o2-1 and liao2345/o2-2. However, the kernel phenotypes of the two o2 NILs were different from each other. liao2345/o2-1 had the wild-type vitreous endosperm, which is similar to its recurrent parent liao2345, while the endosperm of liao2345/o2-2 was opaque, identical to typical o2 mutant individuals. In comparison to their recurrent parent liao2345, the lysine concentration of liao2345/o2-1 was similar and the lysine concentration in liao2345/o2-2 was doubled. SDS-PAGE analysis indicated that liao2345/o2-1 had the same zeins ratio as liao2345, whereas the zeins concentration of liao2345/o2-2 was markedly lower. Sequence and transcript abundance analyses indicated that the CDS of two o2 NILs are derived from CA339, but they have different promoters. The O2 transcript of liao2345/o2-2 is largely inhibited because of an rbg transposable element inserted between the TATA box and initiator codon of liao2345/o2-2. We concluded that different crossing-over patterns during the process of o2 NIL construction resulted in the different kernel phenotypes of the two o2 NILs. We surmise that the reversion of liao2345/o2-1 to wild type was due to the recombination with the wild type liao2345 promoter during introgression and backcrossing. The o2 mutant gene of donor (CA339) is a null mutant because of low O2 expression. However, its CDS probably encodes a protein with normal function which can maintain the normal accumulation of zeins in maize endosperm.
[Show abstract][Hide abstract] ABSTRACT: Introgression of favorable alleles from exotic maize (Zea mays L.) germplasm can broaden the narrow genetic base of available temperate germplasm. Development of maize hybrids for the Yellow and Huai river valleys in the Corn Belt of China has always been hampered by the lack of favorable alleles for improving maize yield and quality. Twenty exotic populations from CIMMYT and the United States were evaluated to identify alleles for improving a widely cultivated hybrid, Zheng 58 x Chang 7-2, which represents the predominant heterotic group, PA x Sipingtou. Sixty-three genotypes, comprising 20 populations, two inbred lines (Zheng 58 and Chang 7-2), a single-cross hybrid (Zheng 58 x Chang 7-2), and 40 inbred x population crosses between the parental inbreds and the CIMMYT and U. S. populations were evaluated for grain yield, test weight, and ear height. Several populations from CIMMYT and the United States were identified as potential sources of favorable alleles for traits lacking in the elite hybrid, Zheng 58 x Chang 7-2, for each trait evaluated. Two exotic populations, Pop 49 and Stay green-yellow, were the most outstanding because they possessed favorable alleles for several traits that were not present in the target hybrid evaluated. These results demonstrate that the exotic populations evaluated in this study represent sources of useful genetic variability with good potential for improving Chinese elite germplasm.
No preview · Article · Nov 2013 · Agronomy journal
[Show abstract][Hide abstract] ABSTRACT: Artificial selection during domestication and post-domestication improvement results in loss of genetic diversity near target loci. However, the genetic locus associated with cob glume color and the nature of the genomic pattern surrounding it was elusive and the selection effect in that region was not clear. An association mapping panel consisting of 283 diverse modern temperate maize elite lines was genotyped by a chip containing over 55,000 evenly distributed SNPs. Ten-fold resequencing at the target region on 40 of the panel lines and 47 tropical lines was also undertaken. A genome-wide association study (GWAS) for cob glume color confirmed the P1 locus, which is located on the short arm of chromosome 1, with a − log10P value for surrounding SNPs higher than the Bonferroni threshold (α/n, α < 0.001) when a mixed linear model (MLM) was implemented. A total of 26 markers were identified in a 0.78 Mb region surrounding the P1 locus, including 0.73 Mb and 0.05 Mb upstream and downstream of the P1 gene, respectively. A clear linkage disequilibrium (LD) block was found and LD decayed very rapidly with increasing physical distance surrounding the P1 locus. The estimates of π and Tajima's D were significantly (P < 0.001) lower at both ends compared to the locus. Upon comparison of temperate and tropical lines at much finer resolution by resequencing (180-fold finer than chip SNPs), a more structured LD block pattern was found among the 40 resequenced temperate lines. All evidence indicates that the P1 locus in temperate maize has not undergone neutral evolution but has been subjected to artificial selection during post-domestication selection or improvement. The information and analytical results generated in this study provide insights as to how breeding efforts have affected genome evolution in crop plants.
[Show abstract][Hide abstract] ABSTRACT: Introgression of elite exotic maize (Zea mays L.) germplasm into breeding programs would increase genetic variation within heterotic groups and counter the narrowing of the Chinese germplasm base. This study measured the performance of exotic populations in northern China to allow use of elite germplasm to broaden the genetic base of Chinese germplasm. Fifteen International Maize and Wheat Improvement Center (CIMMYT) and U.S. populations were testcrossed with Csyn 5, Cpop. 11, and Cpop. 12, which represent Chinese Sipingtou, Lancaster Sure crop, and Reid Yellow Dent subgroups, respectively. Forty-five testcrosses and 18 populations were evaluated using Miranda Filho and Geraldi's analysis for variety effects and combining ability for grain yield, stalk lodging, ear height, and days to silking in northern China. The results indicated that additive genetic effects were more important than nonadditive genetic effects for all traits measured. Pop28 and BS29 were most adapted to northern China for grain yield and other adaptation traits, and Pool 26, Pop32, Tuxpeno, and Suwan 1 exhibited more favorable alleles for stalk lodging tolerance and high yield potential. We propose to introgress Pool 26 and Suwan 1 into Sipingtou, BS29 and Pop32 into Lancaster, and Pop28 and Tuxpeno into Reid to enrich the genetic base of Chinese heterotic pools.
[Show abstract][Hide abstract] ABSTRACT: U.S. maize germplasm has been considered as a new alternative source of favorable alleles to broaden the narrowing genetic base of temperate germplasm. However, direct utilization of diverse U.S. germplasm in target mega-environments could be hampered by limited adaptation-related information on parental performance or heterotic response in crosses with local germplasm. The objective of this study was to measure the performance of U.S. maize populations for broadening the Chinese germplasm base. Fifteen diverse U.S. populations were testcrossed to three local tester lines, representing Chinese heterotic groups A, B, and D, to evaluate parental adaptation and combining abilities for days to silking (DS), ear height (EH), and grain yield (GY) in target and intermediate mega-environments in northern China. There was genetic variability among U.S. maize populations for additive and non-additive effects for DS and GY, and predominant additive genetic effects for EH. All 15 U.S. populations, except for BS27 and BS31 due to slightly high EH, could be directly used in target mega-environments similar to the U.S. Corn Belt. U.S. populations BS11(HI)C7, BS13(S)C7, BS17(CB)C4, BS31, BSCB1(R)C12, and BSBB(SRCB)C4 had better effects for increasing GY. Favorable effects for DS were also observed in BS11(HI)C5 and BS31, for DS and EH in BS13(S)C7 and BSCB1(R)C12, and for EH in BSBB(SRCB)C4. The best strategies for utilizing these germplasms may be to introgress BS13(S)C7 and BS17(CB)C4 into group A, BS11(HI)C5 into group B, and BSCB1(R)C12 and BSBB(SRCB)C4 into group D to increase genetic variation within Chinese heterotic pools.
[Show abstract][Hide abstract] ABSTRACT: Kernel weight, controlled by quantitative trait loci (QTL), is an important component of grain yield in maize. Cytokinins (CKs) participate in determining grain morphology and final grain yield in crops. ZmIPT2, which is expressed mainly in the basal transfer cell layer, endosperm, and embryo during maize kernel development, encodes an isopentenyl transferase (IPT) that is involved in CK biosynthesis.
The coding region of ZmIPT2 was sequenced across a panel of 175 maize inbred lines that are currently used in Chinese maize breeding programs. Only 16 single nucleotide polymorphisms (SNPs) and seven haplotypes were detected among these inbred lines. Nucleotide diversity (pi) within the ZmIPT2 window and coding region were 0.347 and 0.0047, respectively, and they were significantly lower than the mean nucleotide diversity value of 0.372 for maize Chromosome 2 (P < 0.01). Association mapping revealed that a single nucleotide change from cytosine (C) to thymine (T) in the ZmIPT2 coding region, which converted a proline residue into a serine residue, was significantly associated with hundred kernel weight (HKW) in three environments (P <0.05), and explained 4.76% of the total phenotypic variation. In vitro characterization suggests that the dimethylallyl diphospate (DMAPP) IPT activity of ZmIPT2-T is higher than that of ZmIPT2-C, as the amounts of adenosine triphosphate (ATP), adenosine diphosphate (ADP), and adenosine monophosphate (AMP) consumed by ZmIPT2-T were 5.48-, 2.70-, and 1.87-fold, respectively, greater than those consumed by ZmIPT2-C. The effects of artificial selection on the ZmIPT2 coding region were evaluated using Tajima's D tests across six subgroups of Chinese maize germplasm, with the most frequent favorable allele identified in subgroup PB (Partner B).
These results showed that ZmIPT2, which is associated with kernel weight, was subjected to artificial selection during the maize breeding process. ZmIPT2-T had higher IPT activity than ZmIPT2-C, and this favorable allele for kernel weight could be used in molecular marker-assisted selection for improvement of grain yield components in Chinese maize breeding programs.
[Show abstract][Hide abstract] ABSTRACT: Maize rough dwarf disease (MRDD, a viral disease) results in significant grain yield losses, while genetic basis of which is largely unknown. Based on comparative genomics, eukaryotic translation initiation factor 4E (eIF4E) was considered as a candidate gene for MRDD resistance, validation of which will help to understand the possible genetic mechanism of this disease. ZmeIF4E (orthologs of eIF4E gene in maize) encodes a protein of 218 amino acids, harboring five exons and no variation in the cDNA sequence is identified between the resistant inbred line, X178 and susceptible one, Ye478. ZmeIF4E expression was different in the two lines plants treated with three plant hormones, ethylene, salicylic acid, and jasmonates at V3 developmental stage, suggesting that ZmeIF4E is more likely to be involved in the regulation of defense gene expression and induction of local and systemic resistance. Moreover, four cis-acting elements related to plant defense responses, including DOFCOREZM, EECCRCAH1, GT1GAMSCAM4, and GT1CONSENSUS were detected in ZmeIF4E promoter for harboring sequence variation in the two lines. Association analysis with 163 inbred lines revealed that one SNP in EECCRCAH1 is significantly associated with CSI of MRDD in two environments, which explained 3.33 and 9.04 % of phenotypic variation, respectively. Meanwhile, one SNP in GT-1 motif was found to affect MRDD resistance only in one of the two environments, which explained 5.17 % of phenotypic variation. Collectively, regulatory motifs respectively harboring the two significant SNPs in ZmeIF4E promoter could be involved in the defense process of maize after viral infection. These results contribute to understand maize defense mechanisms against maize rough dwarf virus.
Full-text · Article · Mar 2013 · MGG Molecular & General Genetics
[Show abstract][Hide abstract] ABSTRACT: Retrospective analyses of genetic yield may provide an understanding of unexploited genetic potential and indicate pathways for future yield improvement, and could be the basis of further study for exploiting molecular mechanisms of yield improvement in the future. The objective of this study is to further examine maize (Zea mays L.) yield trends and describe changes in ear traits and the relationship between grain yield and ear traits from the 1950s to the 2000s in China. Trials were conducted at three locations in 2007 and 2008 and at five locations in 2009. Twenty-seven single-cross hybrids, four double-cross hybrids, and four open-pollinated varieties were grown at three densities at each location in each year. Grain yield potential per plant increased from 141.2 g for the 1950s' open pollination varieties (OPVs) to 306.5 g for the hybrids from the 2000s, and improved significantly from 1950 to 1970 and from 1990 to 2000. Overall, all ear traits tended to increase; however, the degree of improvement in ear traits varied among different eras and different traits. Advances in grain yield were attributable to kernel number per ear and kernel weight from the 1950s to 2000s in China. Kernel number per row, shelling percentage, and percentage barrenness need more improvement, and breeders in China should attempt to achieve gains for kernel number while maintaining kernel weight.
No preview · Article · Jan 2013 · Agronomy journal
[Show abstract][Hide abstract] ABSTRACT: The major quantitative trait locus (QTL) qHS2.09 plays an important role in resistance to head smut during maize breeding and production. In this study, a near-isogenic line (NIL), L34, which harbors the major QTL qHS2.09 in bin 2.09, was developed using a resistant donor 'Mo17' in a susceptible genetic background 'Huangzao4'. Using 18,683 genome-wide polymorphic loci, this major QTL was finely mapped into an interval of ≈1.10 Mb, flanked by single nucleotide polymorphism (SNP) markers PZE-102187307 and PZE-102188421. Moreover, the favorable allele from 'Mo17' for SNP PZE-102187611 in this interval that was most significantly associated with resistance to head smut (P = 1.88 E-10) and accounted for 39.7 to 44.4% of the phenotypic variance in an association panel consisting of 80 inbred lines. With combined linkage and association mapping, this major QTL was finally located between SNP PZE-102187486 and PZE-102188421 with an interval of ≈1.00 Mb. Based on the pedigrees of 'Mo17' and its derivatives widely used in temperate maize breeding programs, the favorable haplotype from 'Mo17' is shown to be the main source of resistance to head smut in these lines. Therefore, the SNPs closely linked to the major QTL qHS2.09, detected in both linkage and association mapping, and could be useful for marker-assisted selection in maize breeding programs.
[Show abstract][Hide abstract] ABSTRACT: The objective of this investigation was to analyze trends in diseases resistance along with genetic gain. Experimental materials consisted of maize varieties selected from each decade beginning with the 1950s. These varieties were evaluated for resistance to maize dwarf mosaic virus (MDMV), maize rough dwarf virus (MRDV), common smut disease (CSD) and head smut disease (HSD) in several different locations. Artificial inoculation was adopted for infection with MDMV and HSD, whereas natural infection was used for infection MRDV and CSD. Results indicated that resistance of the newer varieties to MDMV, CSD, and HSD was greater than that of older varieties, but the correlation to decades was not significant. To date, no variety tested in China has shown resistance to MRDV, which is likely due to a lack of maize germplasm resources resistant to MRDV in China. So the next goal will be to import new germplasm resources and select resistant germplasm as the basis of breeding resistant varieties.
[Show abstract][Hide abstract] ABSTRACT: The harvest index for many crops can be improved through introduction of dwarf stature to increase lodging resistance, combined with early maturity. The inbred line Shen5003 has been widely used in maize breeding in China as a key donor line for the dwarf trait. Also, one major quantitative trait locus (QTL) controlling plant height has been identified in bin 5.05-5.06, across several maize bi-parental populations. With the progress of publicly available maize genome sequence, the objective of this work was to identify the candidate genes that affect plant height among Chinese maize inbred lines with genome wide association studies (GWAS).
A total of 284 maize inbred lines were genotyped using over 55,000 evenly spaced SNPs, from which a set of 41,101 SNPs were filtered with stringent quality control for further data analysis. With the population structure controlled in a mixed linear model (MLM) implemented with the software TASSEL, we carried out a genome-wide association study (GWAS) for plant height. A total of 204 SNPs (P≤0.0001) and 105 genomic loci harboring coding regions were identified. Four loci containing genes associated with gibberellin (GA), auxin, and epigenetic pathways may be involved in natural variation that led to a dwarf phenotype in elite maize inbred lines. Among them, a favorable allele for dwarfing on chromosome 5 (SNP PZE-105115518) was also identified in six Shen5003 derivatives.
The fact that a large number of previously identified dwarf genes are missing from our study highlights the discovery of the consistently significant association of the gene harboring the SNP PZE-105115518 with plant height (P=8.91e-10) and its confirmation in the Shen5003 introgression lines. Results from this study suggest that, in the maize breeding schema in China, specific alleles were selected, that have played important roles in maize production.
[Show abstract][Hide abstract] ABSTRACT: Nitrate is the major source of nitrogen available for many crop plants and is often the limiting factor for plant growth and agricultural productivity especially for maize. Many studies have been done identifying the transcriptome changes under low nitrate conditions. However, the microRNAs (miRNAs) varied under nitrate limiting conditions in maize has not been reported. MiRNAs play important roles in abiotic stress responses and nutrient deprivation.
In this study, we used the SmartArray™ and GeneChip® microarray systems to perform a genome-wide search to detect miRNAs responding to the chronic and transient nitrate limiting conditions in maize. Nine miRNA families (miR164, miR169, miR172, miR397, miR398, miR399, miR408, miR528, and miR827) were identified in leaves, and nine miRNA families (miR160, miR167, miR168, miR169, miR319, miR395, miR399, miR408, and miR528) identified in roots. They were verified by real time stem loop RT-PCR, and some with additional time points of nitrate limitation. The miRNAs identified showed overlapping or unique responses to chronic and transient nitrate limitation, as well as tissue specificity. The potential target genes of these miRNAs in maize were identified. The expression of some of these was examined by qRT-PCR. The potential function of these miRNAs in responding to nitrate limitation is described.
Genome-wide miRNAs responding to nitrate limiting conditions in maize leaves and roots were identified. This provides an insight into the timing and tissue specificity of the transcriptional regulation to low nitrate availability in maize. The knowledge gained will help understand the important roles miRNAs play in maize responding to a nitrogen limiting environment and eventually develop strategies for the improvement of maize genetics.