[Show abstract][Hide abstract] ABSTRACT: In addition to single-nucleotide polymorphisms, structural variation is abundant in many plant genomes. The structural variation across a species can be represented by a 'pan-genome', which is essential to fully understand the genetic control of phenotypes. However, the pan-genome's complexity hinders its accurate assembly via sequence alignment. Here we demonstrate an approach to facilitate pan-genome construction in maize. By performing 18 trillion association tests we map 26 million tags generated by reduced representation sequencing of 14,129 maize inbred lines. Using machine-learning models we select 4.4 million accurately mapped tags as sequence anchors, 1.1 million of which are presence/absence variations. Structural variations exhibit enriched association with phenotypic traits, indicating that it is a significant source of adaptive variation in maize. The ability to efficiently map ultrahigh-density pan-genome sequence anchors enables fine characterization of structural variation and will advance both genetic research and breeding in many crops.
[Show abstract][Hide abstract] ABSTRACT: Plant architecture is a key factor for high productivity maize because ideal plant architecture with an erect leaf angle and optimum leaf orientation value allow for more efficient light capture during photosynthesis and better wind circulation under dense planting conditions. To extend our understanding of the genetic mechanisms involved in leaf-related traits, three connected recombination inbred line (RIL) populations including 538 RILs were genotyped by genotyping-by-sequencing (GBS) method and phenotyped for the leaf angle and related traits in six environments. We conducted single population quantitative trait locus (QTL) mapping and joint linkage analysis based on high-density recombination bin maps constructed from GBS genotype data. A total of 45 QTLs with phenotypic effects ranging from 1.2% to 29.2% were detected for four leaf architecture traits by using joint linkage mapping across the three populations. All the QTLs identified for each trait could explain approximately 60% of the phenotypic variance. Four QTLs were located on small genomic regions where candidate genes were found. Genomic predictions from a genomic best linear unbiased prediction (GBLUP) model explained 45±9% to 68±8% of the variation in the remaining RILs for the four traits. These results extend our understanding of the genetics of leaf traits and can be used in genomic prediction to accelerate plant architecture improvement.
PLoS ONE 03/2015; 10(3):e0121624. DOI:10.1371/journal.pone.0121624 · 3.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: To measure the contributions of parental inbreds per se and heterosis to the genetic gain of single-cross maize (Zea mays L.) hybrids, yield trials of 29 historically important hybrids used in China during 1964 through 2001 and their parental inbreds were conducted. Mean rate of genetic gain for single-cross hybrids when measured across all locations was 55 kg ha(-1) yr(-1); heterosis contributed 37 kg ha(-1) yr(-1) (67%) of yield gain. Inbred yields at stressed locations were exceptionally poor and may have inflated measurements of heterosis. At unstressed locations, heterosis contributed 5 kg ha(-1) yr(-1) (8%) and 16 kg ha(-1) yr(-1) (39%) or 10 kg ha(-1) yr(-1) (19%) when locations were combined. For individual characteristics, the highest percent heterosis was for kernel weight per ear (58.6%), corresponding to and emphasizing the historic goal in China of increasing yield on an individual plant rather than on a unit area basis. There are opportunities to further improve the productivity of Chinese maize by increasing inbred parent yields, increasing tolerances to stresses associated with higher planting densities, and also increasing the contribution of heterosis through optimal assignation of inbreds into complementary heterotic groups.
[Show abstract][Hide abstract] ABSTRACT: To investigate the genetic structure of Chinese maize germplasm, the MaizeSNP50 BeadChip with 56,110 single nucleotide polymorphisms (SNPs) was used to genotype a collection of 367 inbred lines widely used in maize breeding of China. A total of 41,819 informative SNPs with minor allele number of more than 0.05 were used to estimate the genetic diversity, relatedness, and linkage disequilibrium (LD) decay. Totally 1,015 SNPs evenly distributed in the genome were selected randomly to evaluate the population structure of these accessions. Results showed that two main groups could be determined i.e., the introduced germplasm and the local germplasm. Further, five subgroups corresponding to different heterotic groups, that is, Reid Yellow Dent (Reid), Lancaster Sure Crop (Lancaster), P group (P), Tang Sipingtou (TSPT), and Tem-tropic I group (Tem-tropic I), were determined. The genetic diversity of within subgroups was highest in the Tem-Tropic I and lowest in the P. Most lines in this panel showed limited relatedness with each other. Comparisons of gene diversity showed that there existed some conservative genetic regions in specific subgroups across the ten chromosomes, i.e., seven in the Lancaster, seven in the Reid, six in the TSPT, five in the P, and two in the Tem-Tropical I. In addition, the results also revealed that there existed fifteen conservative regions transmitted from Huangzaosi, an important foundation parent, to its descendants. These are important for further studies since the outcomes may provide clues to understand why Huangzaosi could become a foundation parent in Chinese maize breeding. For the panel of 367 elite lines, average LD distance was 391 kb and varied among different chromosomes as well as in different genomic regions of one chromosome. This analysis uncovered a high natural genetic diversity in the elite maize inbred set, suggesting that the panel can be used in association study, esp. for temperate regions.
[Show abstract][Hide abstract] ABSTRACT: SbSNAC1 is a member of the plant-specific NAC transcription factor superfamily that plays an important role in the abiotic stress response in sorghum. The SbSNAC1 protein consists of a typical NAC conserved domain at its N terminus and a diverse C-terminal region. The expression of SbSNAC1 was induced by various abiotic stresses, such as drought and salinity. SbSNAC1 is also expressed at a relatively higher concentration in roots and responds to the phytohormone abscisic acid. Transactivation analysis indicated that the transactivation activity of SbSNAC1 is located in the C-terminal region, whereas no activity was detected in the conserved NAC-domain, localized in the N-terminus. Subcellular localization assays using constructs of different SbSNAC1 fragments fused with green fluorescent protein revealed that the SbSNAC1 protein localized in the nucleus, and that the nuclear localization signal was present in the N-terminal section. Furthermore, transgenic plants overexpressing SbSNAC1 had an improved drought stress tolerance compared with wild-type plants, but no obvious retardation was detected in plant growth and development. These results suggest that SbSNAC1 has the potential to improve abiotic stress tolerance.
Plant Cell Tissue and Organ Culture 12/2013; 115(3). DOI:10.1007/s11240-013-0375-2 · 2.61 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Grain yield is one of the most important and complex quantitative traits in maize breeding. In the present study, a total of 11 connected RIL populations, derived from crosses between elite inbreed “Huangzaosi” as the common parent and 11 elite inbreeds, were evaluated for five yield components and kernel-related traits under six environments. Quantitative trait loci (QTL) were detected for the traits under each environment and in joint analysis across all environments for each population. A total of 146 major QTL with R2 > 10 % in at least one environment and also detected based on joint analysis across all environments were identified in the 11 populations. Lqkwei4 conferring kernel weight and Lqklen4-1 conferring kernel length both located in the adjacent marker intervals in bin 4.05 were stably expressed in four environments and in joint analysis across six environments, with the largest R2 over 27 and 24 % in a single environment, respectively. Moreover, all major QTL detected in the 11 populations were aligned on the IBM2 2008 neighbors reference map. Totally 16 common QTL (CQTL) were detected. Seven important CQTL (CQTL1-2, CQTL1-3, CQTL4-1, CQTL4-2, CQTL4-3, CQTL4-4, and CQTL6-1) were located in bin 1.07, 1.10, 4.03, 4.05, 4.08, 4.09 and 6.01–6.02, respectively. These chromosomal regions could be targets for fine mapping and marker-assisted selection.
[Show abstract][Hide abstract] ABSTRACT: Large ex situ collections require approaches for sampling manageable amounts of germplasm for in-depth characterization and use. We present here a large diversity survey in sorghum with 3367 accessions and 41 reference nuclear SSR markers. Of 19 alleles on average per locus, the largest numbers of alleles were concentrated in central and eastern Africa. Cultivated sorghum appeared structured according to geographic regions and race within region. A total of 13 groups of variable size were distinguished. The peripheral groups in western Africa, southern Africa and eastern Asia were the most homogeneous and clearly differentiated. Except for Kafir, there was little correspondence between races and marker-based groups. Bicolor, Caudatum, Durra and Guinea types were each dispersed in three groups or more. Races should therefore better be referred to as morphotypes. Wild and weedy accessions were very diverse and scattered among cultivated samples, reinforcing the idea that large gene-flow exists between the different compartments. Our study provides an entry to global sorghum germplasm collections. Our reference marker kit can serve to aggregate additional studies and enhance international collaboration. We propose a core reference set in order to facilitate integrated phenotyping experiments towards refined functional understanding of sorghum diversity.
PLoS ONE 04/2013; 8(4):e59714. DOI:10.1371/journal.pone.0059714 · 3.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Simultaneous improvement in grain yield and related traits in maize hybrids and their parents (inbred lines) requires a better knowledge of genotypic correlations between family per se performance (FP) and testcross performance (TP). Thus, to understand the genetic basis of yield-related traits in both inbred lines and their testcrosses, two F (2:3) populations (including 230 and 235 families, respectively) were evaluated for both FP and TP of eight yield-related traits in three diverse environments. Genotypic correlations between FP and TP, [Formula: see text] (FP, TP), were low (0-0.16) for grain yield per plant (GYPP) and kernel number per plant (KNPP) in the two populations, but relatively higher (0.32-0.69) for the other six traits with additive effects as the primary gene action. Similar results were demonstrated by the genotypic correlations between observed and predicted TP values based on quantitative trait loci positions and effects for FP, [Formula: see text] (M (FP), Y (TP)). A total of 88 and 35 QTL were detected with FP and TP, respectively, across all eight traits in the two populations. However, the genotypic variances explained by the QTL detected in the cross-validation analysis were much lower than those in the whole data set for all traits. Several common QTL between FP and TP that accounted for large phenotypic variances were clustered in four genomic regions (bin 1.10, 4.05-4.06, 9.02, and 10.04), which are promising candidate loci for further map-based cloning and improvement in grain yield in maize. Compared with publicly available QTL data, these QTL were also detected in a wide range of genetic backgrounds and environments in maize. These results imply that effective selection based on FP to improve TP could be achieved for traits with prevailing additive effects.
[Show abstract][Hide abstract] ABSTRACT: NAC proteins are plant-specific transcription factors that play essential roles in stress responses. However, only little information regarding stress-related NAC genes is available in maize. In this study, a maize NAC gene, ZmSNAC1, was cloned and functionally characterized. Expression analysis revealed that ZmSNAC1 was strongly induced by low temperature, high-salinity, drought stress, and abscisic acid (ABA) treatment, but downregulated by salicylic acid treatment. Subcellular localization experiments in Arabidopsis protoplast cells indicated that ZmSNAC1 was localized in the nucleus. Transactivation assays demonstrated that ZmSNAC1 functioned as a transcriptional activator. Overexpression of ZmSNAC1 in Arabidopsis led to hypersensitivity to ABA and osmotic stress at the germination stage, but enhanced tolerance to dehydration compared to wild-type seedlings. These results suggest that ZmSNAC1 functions as a stress-responsive transcription factor in positive modulation of abiotic stress tolerance, and may have applications in the engineering of drought-tolerant crops. KEY MESSAGE: ZmSNAC1 functioned as a stress-responsive transcription factor in response to abiotic stresses, and might be useful for crop tolerance improvement.
[Show abstract][Hide abstract] ABSTRACT: MADS-box genes encode a family of transcription factors, which control diverse developmental processes in flowering plants, with organs ranging from roots, flowers and fruits. In this study, six maize cDNAs encoding MADS-box proteins were isolated. BLASTX searches and phylogenetic analysis indicated that the six MADS-box genes belonging to the AGL2-like clade. qRT-PCR analysis revealed that these genes had differential expression patterns in different organs in maize. The results of yeast one-hybrid system indicated that the protein ZMM3-1, ZMM3-2, ZMM6, ZMM7-L, ZMM8-L and ZMM14-L had transcriptional activation activity. Subcellular localization of ZMM7-L demonstrated that the fluorescence of ZMM7-L-GFP was mainly detected in the nuclei of onion epidermal cells. qRT-PCR analysis for expression pattern of ZMM7-L showed that the gene was up-regulated by abiotic stresses and down-regulated by exogenous ABA. The germination rates of over-expression transgenic lines were lower than that of the wild type on medium with 150 mM NaCl, 350 mM mannitol. These results indicated that ZMM7-L might be a negative transcription factor responsive to abiotic stresses.
[Show abstract][Hide abstract] ABSTRACT: Plasma membrane protein 3 (PMP3), a class of small hydrophobic polypeptides with high sequence similarity, is responsible for salt, drought, cold, and abscisic acid. These small hydrophobic ploypeptides play important roles in maintenance of ion homeostasis. In this study, eight ZmPMP3 genes were cloned from maize and responsive to salt, drought, cold and abscisic acid. The eight ZmPMP3s were membrane proteins and their sequences in trans-membrane regions were highly conserved. Phylogenetic analysis showed that they were categorized into three groups. All members of group II were responsive to ABA. Functional complementation showed that with the exception of ZmPMP3-6, all were capable of maintaining membrane potential, which in turn allows for regulation of intracellular ion homeostasis. This process was independent of the presence of Ca(2+). Lastly, over-expression of ZmPMP3-1 enhanced growth of transgenic Arabidopsis under salt condition. Through expression analysis of deduced downstream genes in transgenic plants, expression levels of three ion transporter genes and four important antioxidant genes in ROS scavenging system were increased significantly in transgenic plants during salt stress. This tolerance was likely achieved through diminishing oxidative stress due to the possibility of ZmPMP3-1's involvement in regulation of ion homeostasis, and suggests that the modulation of these conserved small hydrophobic polypeptides could be an effective way to improve salt tolerance in plants.
PLoS ONE 02/2012; 7(2):e31101. DOI:10.1371/journal.pone.0031101 · 3.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: With 2 figures and 4 tablesAbstractThe magnitude of genotypic correlations between family per se and testcross, r^g (per se, TC), is crucial for testing schemes in hybrid breeding as well as improvement of commercial hybrids. The objectives of this study were to identify the r^g (per se, TC), to examine the proportion of common QTL for both types of progenies and to determine the gene action of QTL identified for family per se and their value for the prediction of testcross progenies. Under multi-environments, r^g (per se, TC) were significant and higher than r^p (per se, TC), the phenotypic correlations between family per se and testcross for plant height and ear height in two maize crosses. The final fit for QTL explained 21.6–70.3% phenotypic variance and 24.4–79.4% genotypic variance for family per se. However, in cross-validation analysis (CV), the genotypic variance explained by all QTL was less than 60% for the two traits. Several common QTL (Chr. 1, Chr. 8 and Chr. 10) could be detected for both family per se and TC, which seems feasible to apply marker-assisted selection in maize breeding programmes.
[Show abstract][Hide abstract] ABSTRACT: We compared yield, genetic gain, and morphology for two sets of maize (Zea mays L.) hybrids using yield test plots grown in China at different planting densities. One set comprised 29 Chinese maize hybrids that were individually widely grown in China during 1964 through 2001. A second set comprised U.S. hybrids that were used either during the 1960s or during the 2000s. The U.S. hybrids had higher yields for both 1960s and 2000s comparisons. United States hybrids showed highest genetic gain (81 kg ha(-1)) at the highest planting density (67,550 plants ha(-1)) whereas the highest rate of gain for Chinese hybrids was 62 kg ha(-1) at the medium planting density (52,500 plants ha(-1)). Unlike the Chinese hybrids, U.S. hybrids showed significant interaction with planting density. Chronologically, all hybrids showed morphological changes for many characteristics, often at different rates, and occasionally in different directions. Pedigree and molecular marker data showed U.S. and Chinese hybrids to be very different germplasm with decades-old U.S. germplasm contributing even to recently developed and widely used Chinese hybrids. Chinese maize agricultural production can rapidly and significantly benefit from adopting breeding and agronomic strategies that allow for improved yield under higher planting densities.
[Show abstract][Hide abstract] ABSTRACT: In plants, the bZIP (basic leucine zipper) transcription factors regulate diverse functions, including processes such as plant development and stress response. However, few have been functionally characterized in maize (Zea mays). In this study, we cloned ZmbZIP72, a bZIP transcription factor gene from maize, which had only one copy in the maize genome and harbored three introns. Analysis of the amino acid sequence of ZmbZIP72 revealed a highly conserved bZIP DNA-binding domain in its C-terminal region, and four conserved sequences distributed in N- or C-terminal region. The ZmbZIP72 gene expressed differentially in various organs of maize plants and was induced by abscisic acid, high salinity, and drought treatment in seedlings. Subcellular localization analysis in onion epidermal cells indicated that ZmbZIP72 was a nuclear protein. Transactivation assay in yeast demonstrated that ZmbZIP72 functioned as a transcriptional activator and its N terminus (amino acids 23-63) was necessary for the transactivation activity. Heterologous overexpression of ZmbZIP72 improved drought and partial salt tolerance of transgenic Arabidopsis plants, as determined by physiological analyses of leaf water loss, electrolyte leakage, proline content, and survival rate under stress. In addition, the seeds of ZmbZIP72-overexpressing transgenic plants were hypersensitive to ABA and osmotic stress. Moreover, overexpression of ZmbZIP72 enhanced the expression of ABA-inducible genes such as RD29B, RAB18, and HIS1-3. These results suggest that the ZmbZIP72 protein functions as an ABA-dependent transcription factor in positive modulation of abiotic stress tolerance and may be a candidate gene with potential application in molecular breeding to enhance stress tolerance in crops.
[Show abstract][Hide abstract] ABSTRACT: SnRK2 (sucrose non-fermenting 1-related protein kinases 2) represents a unique family of protein kinase in regulating signaling transduction in plants. Although the regulatory mechanisms of SnRK2 have been well demonstrated in Arabidopsis thaliana, their functions in maize are still unknown. In our study, we cloned an SnRK2 gene from maize, ZmSAPK8, which encoded a putative homolog of the rice SAPK8 protein. ZmSAPK8 had two copies in the maize genome and harbored eight introns in its coding region. We demonstrated that ZmSAPK8 expressed differentially in various organs of maize plants and was up-regulated by high-salinity and drought treatment. A green fluorescent protein (GFP)-tagged ZmSAPK8 showed subcellular localization in the cell membrane, cytoplasm and nucleus. In vitro kinase assays indicated that ZmSAPK8 preferred Mn(2+) to Mg(2+) as cofactor for phosphorylation, and Ser-182 and Thr-183 in activation loop was important for its activity. Heterologous overexpression of ZmSAPK8 in Arabidopsis could significantly strengthen tolerance to salt stress. Under salt treatment, ZmSAPK8-overexpressed transgenic plants exhibited higher germination rate and proline content, low electrolyte leakage and higher survival rate than wild type. Further analysis indicated that transgenic plants showed increased transcription of the stress-related genes, RD29A, RD29B, RAB18, ABI1, DREB2A and P5CS1, under high-salinity conditions. The results demonstrated that ZmSAPK8 was involved in diverse stress signal transduction. Moreover, no obvious adverse effects on growth and development in the ZmSAPK8-overexpressed transgenic plants implied that ZmSAPK8 was potentially useful in transgenic breeding to improve salt tolerance in crops.
[Show abstract][Hide abstract] ABSTRACT: The objectives of this study were to (i) measure genetic gain using a set of maize (Zea mays L.) single-cross hybrids that were widely used in Chinese maize production from 1964 to 2001, (ii) determine if there were changes in morphological characteristics, and (iii) examine the germplasm backgrounds of these hybrids. Yield trials were conducted for 3 yr, using a split-plot design. Each hybrid was planted at three different densities in four locations, two locations each representing summer and spring corn areas. Mean rates of genetic gain were 52 kg ha(-1) yr(-1) when measured at the spring locations, 69 kg ha(-1) yr(-1) when measured at the summer locations, and 60 kg ha(-1) yr(-1) when measured across all locations. There was no significant effect of planting density on genetic gain. Genetic gain has been largely contributed by increased yield per plant and this strategy was reflected in changes in ear and plant morphology. Analyses of pedigree backgrounds showed continuing dependence on U. S. germplasm backgrounds, notably C103, Oh43, Mo17, and Iowa Stiff Stalk Synthetic (BSSS).