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Abstract
Seed size is a key determinant of evolutionary fitness, and is also one of the most important components of seed yield. In angiosperms, seed development begins with double fertilization, which leads to the formation of a diploid embryo and a triploid endosperm. The outermost layer of the seed is the seed coat, which differentiates from maternal integuments. Therefore, the size of a seed is determined by the co-ordinated growth of the embryo, endosperm, and maternal tissue. Recent studies have identified several factors that act maternally or zygotically to regulate seed size, and revealed possible mechanisms that underlie seed size control in Arabidopsis and rice. In this review, we summarize current research progress in maternal control of seed size and discuss the roles of several newly identified regulators in maternal regulation of seed growth.
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Affiliation(s)
- Na Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yunhai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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102
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Wang S, Zhang X, Chen F, Cui D. A Single-Nucleotide Polymorphism of TaGS5 Gene Revealed its Association with Kernel Weight in Chinese Bread Wheat. FRONTIERS IN PLANT SCIENCE 2015; 6:1166. [PMID: 26779195 PMCID: PMC4688388 DOI: 10.3389/fpls.2015.01166] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/07/2015] [Indexed: 05/21/2023]
Abstract
TaGS5 genes were cloned from bread wheat and were physically mapped on 3AS and 3DS. Sequencing results revealed that a SNP was found in the sixth exon of TaGS5-A1 gene. The SNP resulted in amino acid change from alanine to serine at the 303 bp position of TaGS5-A1. These two alleles were designated as TaGS5-A1a (alanine at the 303 bp position) and TaGS5-A1b genes (serine at the 303-bp position). Analysis of association of TaGS5-A1 alleles with agronomic traits indicated that cultivars with TaGS5-A1b possessed wider kernel width and higher thousand-kernel weight, as well as significantly lower plant height, spike length, and internode length below spike than those of cultivars with TaGS5-A1a over 3 years. These trait differences between TaGS5-A1a and TaGS5-A1b genotypes were larger in landraces than in modern cultivars. This finding suggested that TaGS5 gene played an important role in modulating yield-related traits in the landraces, which possibly resulted from numerous superior genes gathering in modern cultivars after strong artificial selection. The preferred TaGS5-A1b haplotype underwent very strong positive selection in Chinese modern wheat breeding, but not in Chinese landraces. Expression analysis of the TaGS5-A1 gene indicated that TaGS5-A1b allele possessed significantly higher expression level than TaGS5-A1b allele in differently developmental seeds. This study could provide relatively superior genotype in view of agronomic traits in wheat breeding programs. Likewise, this study could offer important information for the dissection of molecular and genetic basis of yield-related traits.
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103
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Zanke CD, Ling J, Plieske J, Kollers S, Ebmeyer E, Korzun V, Argillier O, Stiewe G, Hinze M, Neumann F, Eichhorn A, Polley A, Jaenecke C, Ganal MW, Röder MS. Analysis of main effect QTL for thousand grain weight in European winter wheat (Triticum aestivum L.) by genome-wide association mapping. FRONTIERS IN PLANT SCIENCE 2015; 6:644. [PMID: 26388877 PMCID: PMC4555037 DOI: 10.3389/fpls.2015.00644] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 08/03/2015] [Indexed: 05/19/2023]
Abstract
Grain weight, an essential yield component, is under strong genetic control and at the same time markedly influenced by the environment. Genetic analysis of the thousand grain weight (TGW) by genome-wide association study (GWAS) was performed with a panel of 358 European winter wheat (Triticum aestivum L.) varieties and 14 spring wheat varieties using phenotypic data of field tests in eight environments. Wide phenotypic variations were indicated for the TGW with BLUEs (best linear unbiased estimations) values ranging from 35.9 to 58.2 g with a mean value of 45.4 g and a heritability of H(2) = 0.89. A total of 12 candidate genes for plant height, photoperiodism and grain weight were genotyped on all varieties. Only three candidates, the photoperiodism gene Ppd-D1, dwarfing gene Rht-B1and the TaGW-6A gene were significant explaining up to 14.4, 2.3, and 3.4% of phenotypic variation, respectively. For a comprehensive genome-wide analysis of TGW-QTL genotyping data from 732 microsatellite markers and a set of 7769 mapped SNP-markers genotyped with the 90k iSELECT array were analyzed. In total, 342 significant (-log10 (P-value) ≥ 3.0) marker trait associations (MTAs) were detected for SSR-markers and 1195 MTAs (-log10(P-value) ≥ 3.0) for SNP-markers in all single environments plus the BLUEs. After Bonferroni correction, 28 MTAs remained significant for SSR-markers (-log10 (P-value) ≥ 4.82) and 58 MTAs for SNP-markers (-log10 (P-value) ≥ 5.89). Apart from chromosomes 4B and 6B for SSR-markers and chromosomes 4D and 5D for SNP-markers, MTAs were detected on all chromosomes. The highest number of significant SNP-markers was found on chromosomes 3B and 1B, while for the SSRs most markers were significant on chromosomes 6D and 3D. Overall, TGW was determined by many markers with small effects. Only three SNP-markers had R(2) values above 6%.
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Affiliation(s)
- Christine D. Zanke
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
| | - Jie Ling
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
| | | | | | | | | | | | | | | | | | | | | | - Cornelia Jaenecke
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
| | | | - Marion S. Röder
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
- *Correspondence: Marion S. Röder, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, D-06466 Gatersleben, Germany
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104
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Thirunavukkarasu N, Hossain F, Arora K, Sharma R, Shiriga K, Mittal S, Mohan S, Namratha PM, Dogga S, Rani TS, Katragadda S, Rathore A, Shah T, Mohapatra T, Gupta HS. Functional mechanisms of drought tolerance in subtropical maize (Zea mays L.) identified using genome-wide association mapping. BMC Genomics 2014; 15:1182. [PMID: 25539911 PMCID: PMC4367829 DOI: 10.1186/1471-2164-15-1182] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 12/16/2014] [Indexed: 01/25/2023] Open
Abstract
Background Earlier studies were focused on the genetics of temperate and tropical maize under drought. We identified genetic loci and their association with functional mechanisms in 240 accessions of subtropical maize using a high-density marker set under water stress. Results Out of 61 significant SNPs (11 were false-discovery-rate-corrected associations), identified across agronomic traits, models, and locations by subjecting the accessions to water stress at flowering stage, 48% were associated with drought-tolerant genes. Maize gene models revealed that SNPs mapped for agronomic traits were in fact associated with number of functional traits as follows: stomatal closure, 28; flowering, 15; root development, 5; detoxification, 4; and reduced water potential, 2. Interactions of these SNPS through the functional traits could lead to drought tolerance. The SNPs associated with ABA-dependent signalling pathways played a major role in the plant’s response to stress by regulating a series of functions including flowering, root development, auxin metabolism, guard cell functions, and scavenging reactive oxygen species (ROS). ABA signalling genes regulate flowering through epigenetic changes in stress-responsive genes. ROS generated by ABA signalling are reduced by the interplay between ethylene, ABA, and detoxification signalling transductions. Integration of ABA-signalling genes with auxin-inducible genes regulates root development which in turn, maintains the water balance by regulating electrochemical gradient in plant. Conclusions Several genes are directly or indirectly involved in the functioning of agronomic traits related to water stress. Genes involved in these crucial biological functions interacted significantly in order to maintain the primary as well as exclusive functions related to coping with water stress. SNPs associated with drought-tolerant genes involved in strategic biological functions will be useful to understand the mechanisms of drought tolerance in subtropical maize. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1182) contains supplementary material, which is available to authorized users.
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105
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Kim B, Kim DG, Lee G, Seo J, Choi IY, Choi BS, Yang TJ, Kim KS, Lee J, Chin JH, Koh HJ. Defining the genome structure of 'Tongil' rice, an important cultivar in the Korean "Green Revolution". RICE (NEW YORK, N.Y.) 2014; 7:22. [PMID: 26224553 PMCID: PMC4883996 DOI: 10.1186/s12284-014-0022-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 08/28/2014] [Indexed: 05/24/2023]
Abstract
BACKGROUND Tongil (IR667-98-1-2) rice, developed in 1972, is a high-yield rice variety derived from a three-way cross between indica and japonica varieties. Tongil contributed to the self-sufficiency of staple food production in Korea during a period known as the 'Korean Green Revolution'. We analyzed the nucleotide-level genome structure of Tongil rice and compared it to those of the parental varieties. RESULTS A total of 17.3 billion Illumina Hiseq reads, 47× genome coverage, were generated for Tongil rice. Three parental accessions of Tongil rice, two indica types and one japonica type, were also sequenced at approximately 30x genome coverage. A total of 2,149,991 SNPs were detected between Tongil and Nipponbare varieties. The average SNP frequency of Tongil was 5.77 per kb. Genome composition was determined based on SNP data by comparing Tongil with three parental genome sequences using the sliding window approach. Analyses revealed that 91.8% of the Tongil genome originated from the indica parents and 7.9% from the japonica parent. Copy numbers of SSR motifs, ORF gene distribution throughout the whole genome, gene ontology (GO) annotation, and some yield-related QTLs or gene locations were also comparatively analyzed between Tongil and parental varieties using sequence-based tools. Each genetic factor was transferred from the parents into Tongil rice in amounts that were in proportion to the whole genome composition. CONCLUSIONS Tongil was derived from a three-way cross among two indica and one japonica varieties. Defining the genome structure of Tongil rice demonstrates that the Tongil genome is derived primarily from the indica genome with a small proportion of japonica genome introgression. Comparative gene distribution, SSR, GO, and yield-related gene analysis support the finding that the Tongil genome is primarily made up of the indica genome.
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Affiliation(s)
- Backki Kim
- />Department of Plant Science, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-921 South Korea
| | - Dong-Gwan Kim
- />Department of Plant Science, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-921 South Korea
| | - Gileung Lee
- />Department of Plant Science, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-921 South Korea
| | - Jeonghwan Seo
- />Department of Plant Science, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-921 South Korea
| | - Ik-Young Choi
- />National Instrumentation Center for Environmental Management (NICEM, Seoul National University, Seoul, 151-921 South Korea
| | - Beom-Soon Choi
- />National Instrumentation Center for Environmental Management (NICEM, Seoul National University, Seoul, 151-921 South Korea
- />PHYZEN Genome Institute, 501-1, Gwanak Century Tower, 1808 Nambusunhwan-ro, Gwanak-gu, Seoul, 151-836 South Korea
| | - Tae-Jin Yang
- />Department of Plant Science, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-921 South Korea
| | - Kwang Soo Kim
- />Department of Plant Science, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-921 South Korea
| | - Joohyun Lee
- />Department of Applied Bio Science, Konkuk University, Seoul, 143-701 South Korea
| | - Joong Hyoun Chin
- />Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila, 1301 Philippines
| | - Hee-Jong Koh
- />Department of Plant Science, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-921 South Korea
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106
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Radchuk V, Borisjuk L. Physical, metabolic and developmental functions of the seed coat. FRONTIERS IN PLANT SCIENCE 2014; 5:510. [PMID: 25346737 PMCID: PMC4193196 DOI: 10.3389/fpls.2014.00510] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 09/11/2014] [Indexed: 05/04/2023]
Abstract
The conventional understanding of the role of the seed coat is that it provides a protective layer for the developing zygote. Recent data show that the picture is more nuanced. The seed coat certainly represents a first line of defense against adverse external factors, but it also acts as channel for transmitting environmental cues to the interior of the seed. The latter function primes the seed to adjust its metabolism in response to changes in its external environment. The purpose of this review is to provide the reader with a comprehensive view of the structure and functionality of the seed coat, and to expose its hidden interaction with both the endosperm and embryo. Any breeding and/or biotechnology intervention seeking to increase seed size or modify seed features will have to consider the implications on this tripartite interaction.
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Affiliation(s)
| | - Ljudmilla Borisjuk
- Heterosis, Molecular Genetics, Leibniz-Institut für Pflanzengenetik und KulturpflanzenforschungGatersleben, Germany
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107
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Abstract
Grain size is one of the most important factors determining rice yield. As a quantitative trait, grain size is predominantly and tightly controlled by genetic factors. Several quantitative trait loci (QTLs) for grain size have been molecularly identified and characterized. These QTLs may act in independent genetic pathways and, along with other identified genes for grain size, are mainly involved in the signaling pathways mediated by proteasomal degradation, phytohormones, and G proteins to regulate cell proliferation and cell elongation. Many of these QTLs and genes have been strongly selected for enhanced rice productivity during domestication and breeding. These findings have paved new ways for understanding the molecular basis of grain size and have substantial implications for genetic improvement of crops.
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Affiliation(s)
- Jianru Zuo
- State Key Laboratory of Plant Genomics and National Plant Gene Research Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
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108
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Zhao H, Huai Z, Xiao Y, Wang X, Yu J, Ding G, Peng J. Natural variation and genetic analysis of the tiller angle gene MsTAC1 in Miscanthus sinensis. PLANTA 2014; 240:161-75. [PMID: 24771021 DOI: 10.1007/s00425-014-2070-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Accepted: 03/21/2014] [Indexed: 05/25/2023]
Abstract
Biomass yield is an important target trait in Miscanthus breeding for desirable energy crops. Tiller angle is a key trait of plant architecture because it determines planting density and further influences biomass yield through affecting photosynthesis efficiency. TAC1, a major gene involved in tiller and leaf angle control in rice and maize, respectively, has been extensively studied. Nucleotide variation at this gene, MsTAC1, was investigated in 33 Miscanthus sinensis accessions collected from different areas in China, and one genotype of Miscanthus × giganteus. A total of 136 loci, including 129 single base substitutions and seven InDels, occurred within the MsTAC1 gene of 1,874 bp. The genetic diversity at MsTAC1 is characterized by high nucleotide diversity (π value) and high heterozygosity. Clustering analysis indicated that the phylogenetic tree of the 33 M. sinensis accessions was correlated with their geographical sites of origin. The neutrality test revealed no strong selection pressure on coding and non-coding region variations of the MsTAC1 gene in the accessions. Phenotype evaluations were conducted for tiller angle and five other traits in the Miscanthus panels in the first two growth years of 2009 and 2010. Analysis of variance showed significant phenotypic variations in the examined traits. Association analysis using 246 markers detected 88 loci associated with all the test traits in either 1 or 2 years, and 11 of the 88 were year reproducible and thus reliable. These associations indicate that the variation of MsTAC1 affects the phenotypic value of the tiller angle, tiller number and biomass yield, suggesting that allelic variation in MsTAC1 affects multiple traits and demonstrates its significance in Miscanthus breeding programs.
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Affiliation(s)
- Hua Zhao
- National Key Laboratory of Crop Genetic Improvement, Wuhan, 430070, China,
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109
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Hong Y, Chen L, Du LP, Su Z, Wang J, Ye X, Qi L, Zhang Z. Transcript suppression of TaGW2 increased grain width and weight in bread wheat. Funct Integr Genomics 2014; 14:341-9. [PMID: 24890396 DOI: 10.1007/s10142-014-0380-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 05/13/2014] [Accepted: 05/14/2014] [Indexed: 10/25/2022]
Abstract
Bread wheat (Triticum aestivum L.) is a major staple crop in the world. Grain weight is a major factor of grain yield in wheat, and the identification of candidate genes associated with grain weight is very important for high-yield breeding of wheat. TaGW2 is an orthologous gene of rice OsGW2 that negatively regulates the grain width and weight in rice. There are three TaGW2 homoeologs in bread wheat, TaGW2A, TaGW2B, and TaGW2D. In this study, a specific TaGW2-RNA interference (RNAi) cassette was constructed and transformed into a Chinese bread wheat variety 'Shi 4185' with small grain. The transcript levels of TaGW2A, TaGW2B, and TaGW2D were simultaneously downregulated in TaGW2-RNAi transgenic wheat lines. Compared with the controls, TaGW2-underexpressing transgenic lines displayed significantly increases in the grain width and weight, suggesting that TaGW2 negatively regulated the grain width and weight in bread wheat. Further transcript analysis showed that in different bread wheat accessions, the transcript abundance of TaGW2A was negatively associated with the grain width.
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Affiliation(s)
- Yantao Hong
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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110
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Liu Y, Wang L, Sun C, Zhang Z, Zheng Y, Qiu F. Genetic analysis and major QTL detection for maize kernel size and weight in multi-environments. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1019-37. [PMID: 24553962 DOI: 10.1007/s00122-014-2276-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 01/26/2014] [Indexed: 05/11/2023]
Abstract
Twelve major QTL in five optimal clusters and several epistatic QTL are identified for maize kernel size and weight, some with pleiotropic will be promising for fine-mapping and yield improvement. Kernel size and weight are important target traits in maize (Zea mays L.) breeding programs. Here, we report a set of quantitative trait loci (QTL) scattered through the genome and significantly controlled the performance of four kernel traits including length, width, thickness and weight. From the cross V671 (large kernel) × Mc (small kernel), 270 derived F2:3 families were used to identify QTL of maize kernel-size traits and kernel weight in five environments, using composite interval mapping (CIM) for single-environment analysis along with mixed linear model-based CIM for joint analysis. These two mapping strategies identified 55 and 28 QTL, respectively. Among them, 6 of 23 coincident were detected as interacting with environment. Single-environment analysis showed that 8 genetic regions on chromosomes 1, 2, 4, 5 and 9 clustered more than 60 % of the identified QTL. Twelve stable major QTLs accounting for over 10 % of phenotypic variation were included in five optimal clusters on the genetic region of bins 1.02-1.03, 1.04-1.06, 2.05-2.07, 4.07-4.08 and 9.03-9.04; the addition and partial dominance effects of significant QTL play an important role in controlling the development of maize kernel. These putative QTL may have great promising for further fine-mapping with more markers, and genetic improvement of maize kernel size and weight through marker-assisted breeding.
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Affiliation(s)
- Ying Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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111
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Qin L, Hao C, Hou J, Wang Y, Li T, Wang L, Ma Z, Zhang X. Homologous haplotypes, expression, genetic effects and geographic distribution of the wheat yield gene TaGW2. BMC PLANT BIOLOGY 2014; 14:107. [PMID: 24766773 PMCID: PMC4021350 DOI: 10.1186/1471-2229-14-107] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 04/08/2014] [Indexed: 05/19/2023]
Abstract
BACKGROUND TaGW2-6A, cloned in earlier research, strongly influences wheat grain width and TKW. Here, we mainly analyzed haplotypes of TaGW2-6B and their effects on TKW and interaction with haplotypes at TaGW2-6A. RESULTS About 2.9 kb of the promoter sequences of TaGW2-6B and TaGW2-6D were cloned in 34 bread wheat cultivars. Eleven SNPs were detected in the promoter region of TaGW2-6B, forming 4 haplotypes, but no divergence was detected in the TaGW2-6D promoter or coding region. Three molecular markers including CAPS, dCAPS and ACAS, were developed to distinguish the TaGW2-6B haplotypes. Haplotype association analysis indicated that TaGW2-6B has a stronger influence than TaGW2-6A on TKW, and Hap-6B-1 was a favored haplotype increasing grain width and weight that had undergone strong positive selection in global wheat breeding. However, clear geographic distribution differences for TaGW2-6A haplotypes were found; Hap-6A-A was favored in Chinese, Australian and Russian cultivars, whereas Hap-6A-G was preferred in European, American and CIMMYT cultivars. This difference might be caused by a flowering and maturity time difference between the two haplotypes. Hap-6A-A is the earlier type. Haplotype interaction analysis between TaGW2-6A and TaGW2-6B showed additive effects between the favored haplotypes. Hap-6A-A/Hap-6B-1 was the best combination to increase TKW. Relative expression analysis of the three TaGW2 homoeologous genes in 22 cultivars revealed that TaGW2-6A underwent the highest expression. TaGW2-6D was the least expressed during grain development and TaGW2-6B was intermediate. Diversity of the three genes was negatively correlated with their effect on TKW. CONCLUSIONS Genetic effects, expression patterns and historic changes of haplotypes at three homoeologous genes of TaGW2 influencing yield were dissected in wheat cultivars. Strong and constant selection to favored haplotypes has been found in global wheat breeding during the past century. This research also provides a valuable case for understanding interaction of genes that control complex traits in polyploid species.
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Affiliation(s)
- Lin Qin
- Key Laboratory of Crop Gene Resources and Germplasm Enhancment, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Crop Genomics and Bioinformatics Center and National Key Lab of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancment, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jian Hou
- Key Laboratory of Crop Gene Resources and Germplasm Enhancment, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuquan Wang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancment, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tian Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancment, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lanfen Wang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancment, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhengqiang Ma
- Crop Genomics and Bioinformatics Center and National Key Lab of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Xueyong Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancment, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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112
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Li N, Li Y. Ubiquitin-mediated control of seed size in plants. FRONTIERS IN PLANT SCIENCE 2014; 5:332. [PMID: 25071811 PMCID: PMC4093792 DOI: 10.3389/fpls.2014.00332] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 06/24/2014] [Indexed: 05/18/2023]
Abstract
Seed size in higher plants is an important agronomic trait, and is also crucial for evolutionary fitness. In flowering plants, the seed comprises three major anatomical components, the embryo, the endosperm and the seed coat, each with different genetic compositions. Therefore, seed size is coordinately determined by the growth of the embryo, endosperm and maternal tissue. Recent studies have revealed multiple pathways that influence seed size in plants. Several factors involved in ubiquitin-related activities have been recently known to determine seed size in Arabidopsis and rice. In this review, we summarize current knowledge of ubiquitin-mediated control of seed size and discuss the role of the ubiquitin pathway in seed size control.
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Affiliation(s)
| | - Yunhai Li
- *Correspondence: Yunhai Li, Institute of Genetics and Developmental Biology, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China e-mail:
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113
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Lenser T, Theißen G. Molecular mechanisms involved in convergent crop domestication. TRENDS IN PLANT SCIENCE 2013; 18:704-14. [PMID: 24035234 DOI: 10.1016/j.tplants.2013.08.007] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 08/12/2013] [Accepted: 08/21/2013] [Indexed: 05/21/2023]
Abstract
Domestication has helped to understand evolution. We argue that, vice versa, novel insights into evolutionary principles could provide deeper insights into domestication. Molecular analyses have demonstrated that convergent phenotypic evolution is often based on molecular changes in orthologous genes or pathways. Recent studies have revealed that during plant domestication the causal mutations for convergent changes in key traits are likely to be located in particular genes. These insights may contribute to defining candidate genes for genetic improvement during the domestication of new plant species. Such efforts may help to increase the range of arable crops available, thus increasing crop biodiversity and food security to help meet the predicted demands of the continually growing global population under rapidly changing environmental conditions.
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Affiliation(s)
- Teresa Lenser
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, D-07743 Jena, Germany
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114
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Liu S, Wang X, Wang H, Xin H, Yang X, Yan J, Li J, Tran LSP, Shinozaki K, Yamaguchi-Shinozaki K, Qin F. Genome-wide analysis of ZmDREB genes and their association with natural variation in drought tolerance at seedling stage of Zea mays L. PLoS Genet 2013; 9:e1003790. [PMID: 24086146 PMCID: PMC3784558 DOI: 10.1371/journal.pgen.1003790] [Citation(s) in RCA: 177] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 07/26/2013] [Indexed: 12/04/2022] Open
Abstract
The worldwide production of maize (Zea mays L.) is frequently impacted by water scarcity and as a result, increased drought tolerance is a priority target in maize breeding programs. While DREB transcription factors have been demonstrated to play a central role in desiccation tolerance, whether or not natural sequence variations in these genes are associated with the phenotypic variability of this trait is largely unknown. In the present study, eighteen ZmDREB genes present in the maize B73 genome were cloned and systematically analyzed to determine their phylogenetic relationship, synteny with rice, maize and sorghum genomes; pattern of drought-responsive gene expression, and protein transactivation activity. Importantly, the association between the nucleic acid variation of each ZmDREB gene with drought tolerance was evaluated using a diverse population of maize consisting of 368 varieties from tropical and temperate regions. A significant association between the genetic variation of ZmDREB2.7 and drought tolerance at seedling stage was identified. Further analysis found that the DNA polymorphisms in the promoter region of ZmDREB2.7, but not the protein coding region itself, was associated with different levels of drought tolerance among maize varieties, likely due to distinct patterns of gene expression in response to drought stress. In vitro, protein-DNA binding assay demonstrated that ZmDREB2.7 protein could specifically interact with the target DNA sequences. The transgenic Arabidopsis overexpressing ZmDREB2.7 displayed enhanced tolerance to drought stress. Moreover, a favorable allele of ZmDREB2.7, identified in the drought-tolerant maize varieties, was effective in imparting plant tolerance to drought stress. Based upon these findings, we conclude that natural variation in the promoter of ZmDREB2.7 contributes to maize drought tolerance, and that the gene and its favorable allele may be an important genetic resource for the genetic improvement of drought tolerance in maize. Water scarcity is one of the most severe threats to maize production worldwide. Although research has demonstrated that DREB-type transcription factors play important roles in plant water stress response, whether the specific genetic variants in DREB genes contribute to plant drought tolerance is largely unknown. Taking advantages of recent technical and methodological advance, we systematically analyzed all the functional DREB genes in maize and examined their associations with the natural variation in drought tolerance of 368 maize varieties collected from tropical and temperate regions. A significant association in the ZmDREB2.7 gene with drought tolerance was detected in that the DNA polymorphisms in the gene promoter region, but not those in the protein coding region, contributed to observed variations in maize drought tolerance, probably due to the distinct gene expression patterns in response to the stress. Overexpressing ZmDREB2.7 in Arabidopsis resulted in enhanced tolerance to drought stress. Moreover, a favorable ZmDREB2.7 allele, identified from drought-tolerant varieties, was effective in improving plant tolerance to drought stress when it was introduced into a drought-sensitive background. ZmDREB2.7 and its favorable allele represent a valuable genetic resource for enhancing maize drought tolerance by marker assisted breeding and transformation technology.
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Affiliation(s)
- Shengxue Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Graduate University of the Chinese Academy of Sciences, Beijing, China
| | - Xianglan Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Graduate University of the Chinese Academy of Sciences, Beijing, China
| | - Hongwei Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Graduate University of the Chinese Academy of Sciences, Beijing, China
| | - Haibo Xin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiaohong Yang
- National Maize Improvement Center of China, China Agricultural University, Beijing, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jiansheng Li
- National Maize Improvement Center of China, China Agricultural University, Beijing, China
| | - Lam-Son Phan Tran
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, Suehiro-cho, Tsurumi-ku, Yokohama, Japan
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Suehiro-cho, Tsurumi-ku, Yokohama, Japan
| | - Kazuko Yamaguchi-Shinozaki
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Feng Qin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- * E-mail:
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Weng J, Li B, Liu C, Yang X, Wang H, Hao Z, Li M, Zhang D, Ci X, Li X, Zhang S. A non-synonymous SNP within the isopentenyl transferase 2 locus is associated with kernel weight in Chinese maize inbreds (Zea mays L.). BMC PLANT BIOLOGY 2013; 13:98. [PMID: 23826856 PMCID: PMC3704264 DOI: 10.1186/1471-2229-13-98] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 07/02/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND 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. RESULTS 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 (π) 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). CONCLUSIONS 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.
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Affiliation(s)
- Jianfeng Weng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Bo Li
- Shenyang Agricultural University, Shenyang 110161, China
| | - Changlin Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Xiaoyan Yang
- Chongqing Academy of Agricultural Sciences, Chongqing 409912, China
| | - Hongwei Wang
- Shenyang Agricultural University, Shenyang 110161, China
| | - Zhuanfang Hao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Mingshun Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Degui Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Xiaoke Ci
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Xinhai Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Shihuang Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
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Huang R, Jiang L, Zheng J, Wang T, Wang H, Huang Y, Hong Z. Genetic bases of rice grain shape: so many genes, so little known. TRENDS IN PLANT SCIENCE 2013; 18:218-26. [PMID: 23218902 DOI: 10.1016/j.tplants.2012.11.001] [Citation(s) in RCA: 187] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 10/27/2012] [Accepted: 11/01/2012] [Indexed: 05/21/2023]
Abstract
Rice (Oryza sativa) grain shape is a key determinant of grain yield and market values. Facilitated by advancements in genomics and various molecular markers, more than 400 quantitative trait loci (QTLs) associated with rice grain traits have been identified. In this review, we examine the genetic bases of rice grain shape, focusing on the protein products of 13 genes that have been cloned and the chromosome locations of 15 QTLs that have been fine mapped. Although more genes affecting grain traits are likely to be cloned in the near future, characterizing their functions at the biochemical level and applying these molecular data to rice breeding programs will be a more challenging task.
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Affiliation(s)
- Rongyu Huang
- School of Life Sciences, Xiamen University, Xiamen 361005, China
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117
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Zhang K, Wang J, Zhang L, Rong C, Zhao F, Peng T, Li H, Cheng D, Liu X, Qin H, Zhang A, Tong Y, Wang D. Association analysis of genomic loci important for grain weight control in elite common wheat varieties cultivated with variable water and fertiliser supply. PLoS One 2013; 8:e57853. [PMID: 23469248 PMCID: PMC3587626 DOI: 10.1371/journal.pone.0057853] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 01/27/2013] [Indexed: 11/18/2022] Open
Abstract
Grain weight, an essential yield component, is under strong genetic control and markedly influenced by the environment. Here, by genome-wide association analysis with a panel of 94 elite common wheat varieties, 37 loci were found significantly associated with thousand-grain weight (TGW) in one or more environments differing in water and fertiliser levels. Five loci were stably associated with TGW under all 12 environments examined. Their elite alleles had positive effects on TGW. Four, two, three, and two loci were consistently associated with TGW in the irrigated and fertilised (IF), rainfed (RF), reduced nitrogen (RN), and reduced phosphorus (RP) environments. The elite alleles of the IF-specific loci enhanced TGW under well-resourced conditions, whereas those of the RF-, RN-, or RP-specific loci conferred tolerance to the TGW decrease when irrigation, nitrogen, or phosphorus were reduced. Moreover, the elite alleles of the environment-independent and -specific loci often acted additively to enhance TGW. Four additional loci were found associated with TGW in specific locations, one of which was shown to contribute to the TGW difference between two experimental sites. Further analysis of 14 associated loci revealed that nine affected both grain length and width, whereas the remaining loci influenced either grain length or width, indicating that these loci control grain weight by regulating kernel size. Finally, the elite allele of Xpsp3152 frequently co-segregated with the larger grain haplotype of TaGW2-6A, suggesting probable genetic and functional linkages between Xpsp3152 and GW2 that are important for grain weight control in cereal plants. Our study provides new knowledge on TGW control in elite common wheat lines, which may aid the improvement of wheat grain weight trait in further research.
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Affiliation(s)
- Kunpu Zhang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Junjun Wang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Liyi Zhang
- Guizhou Institute of Upland Crops, Guiyang, China
| | - Chaowu Rong
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Fengwu Zhao
- Dry-Land Farming Institute, Hebei Academy of Agricultural and Forestry Sciences, Hengshui, China
| | - Tao Peng
- Jiyuan Institute of Agricultural Sciences, Jiyuan, China
| | - Huimin Li
- Dry-Land Farming Institute, Hebei Academy of Agricultural and Forestry Sciences, Hengshui, China
| | - Dongmei Cheng
- Jiyuan Institute of Agricultural Sciences, Jiyuan, China
| | - Xin Liu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Huanju Qin
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Aimin Zhang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yiping Tong
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Daowen Wang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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118
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Kesavan M, Song JT, Seo HS. Seed size: a priority trait in cereal crops. PHYSIOLOGIA PLANTARUM 2013; 147:113-20. [PMID: 22680622 DOI: 10.1111/j.1399-3054.2012.01664.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Revised: 05/12/2012] [Accepted: 05/15/2012] [Indexed: 05/21/2023]
Abstract
Crop production and productivity must be increased to provide a balanced diet for the global population. The entire genome sequences of crop species allow the elucidation of genes that regulate important traits related to the final crop seed yield, which frequently depends mainly on seed size. Seed size is a major factor that controls seed quantity and it is strongly affected by various biotic, abiotic and genetic factors. Epigenetic marks in the genome and phytohormones are also important factors affecting seed growth and development. Several genes are known to be involved in the control of seed size, but their interaction and functional characterization have yet to be resolved. In this review, we discuss the different factors that govern seed size in cereal crops and Arabidopsis.
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Affiliation(s)
- Markkandan Kesavan
- Department of Plant Science, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
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119
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Sreenivasulu N, Wobus U. Seed-development programs: a systems biology-based comparison between dicots and monocots. ANNUAL REVIEW OF PLANT BIOLOGY 2013; 64:189-217. [PMID: 23451786 DOI: 10.1146/annurev-arplant-050312-120215] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Seeds develop differently in dicots and monocots, especially with respect to the major storage organs. High-resolution transcriptome data have provided the first insights into the molecular networks and pathway interactions that function during the development of individual seed compartments. Here, we review mainly recent data obtained by systems biology-based approaches, which have allowed researchers to construct and model complex metabolic networks and fluxes and identify key limiting steps in seed development. Comparative coexpression network analyses define evolutionarily conservative (FUS3/ABI3/LEC1) and divergent (LEC2) networks in dicots and monocots. Finally, we discuss the determination of seed size--an important yield-related characteristic--as mediated by a number of processes (maternal and epigenetic factors, fine-tuned regulation of cell death in distinct seed compartments, and endosperm growth) and underlying genes defined through mutant analyses. Altogether, systems approaches can make important contributions toward a more complete and holistic knowledge of seed biology and thus support strategies for knowledge-based molecular breeding.
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Affiliation(s)
- Nese Sreenivasulu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Germany.
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120
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Bednarek J, Boulaflous A, Girousse C, Ravel C, Tassy C, Barret P, Bouzidi MF, Mouzeyar S. Down-regulation of the TaGW2 gene by RNA interference results in decreased grain size and weight in wheat. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:5945-55. [PMID: 22996678 DOI: 10.1093/jxb/ers249] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
For important food crops such as wheat and rice, grain yield depends on grain number and size. In rice (Oryza sativa), GW2 was isolated from a major quantitative trait locus for yield and encodes an E3 RING ligase that negatively regulates grain size. Wheat (Triticum aestivum) has TaGW2 homologues in the A, B, and D genomes, and polymorphisms in TaGW2-A were associated with grain width. Here, to investigate TaGW2 function, RNA interference (RNAi) was used to down-regulate TaGW2 transcript levels. Transgenic wheat lines showed significantly decreased grain size-related dimensions compared with controls. Furthermore, TaGW2 knockdown also caused a significant reduction in endosperm cell number. These results indicate that TaGW2 regulates grain size in wheat, possibly by controlling endosperm cell number. Wheat and rice GW2 genes thus seem to have divergent functions, with rice GW2 negatively regulating grain size and TaGW2 positively regulating grain size. Analysis of transcription of TaGW2 homoeologues in developing grains suggested that TaGW2-A and -D act in both the division and late grain-filling phases. Furthermore, biochemical and molecular analyses revealed that TaGW2-A is a functional E3 RING ubiquitin ligase with nucleocytoplasmic subcellular partitioning. A functional nuclear export sequence responsible for TaGW2-A export from the nucleus to the cytosol and retention in the nucleolus was identified. Therefore, these results show that TaGW2 acts in the regulation of grain size and may provide an important tool for enhancement of grain yield.
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Affiliation(s)
- Julie Bednarek
- Université Blaise Pascal, UMR 1095 GDEC, 24 avenue des Landais, F-63177 Aubière, France
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121
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Weng J, Liu X, Wang Z, Wang J, Zhang L, Hao Z, Xie C, Li M, Zhang D, Bai L, Liu C, Zhang S, Li X. Molecular mapping of the major resistance quantitative trait locus qHS2.09 with simple sequence repeat and single nucleotide polymorphism markers in maize. PHYTOPATHOLOGY 2012; 102:692-9. [PMID: 22439860 DOI: 10.1094/phyto-12-11-0330] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
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.
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Affiliation(s)
- Jianfeng Weng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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122
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Genome-wide association study identifies candidate genes that affect plant height in Chinese elite maize (Zea mays L.) inbred lines. PLoS One 2011; 6:e29229. [PMID: 22216221 PMCID: PMC3247246 DOI: 10.1371/journal.pone.0029229] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Accepted: 11/22/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND 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). METHODS AND FINDINGS 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. CONCLUSIONS 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.
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123
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Chen J, Chang SX, Anyia AO. Gene discovery in cereals through quantitative trait loci and expression analysis in water-use efficiency measured by carbon isotope discrimination. PLANT, CELL & ENVIRONMENT 2011; 34:2009-23. [PMID: 21752030 DOI: 10.1111/j.1365-3040.2011.02397.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Drought continues to be a major constraint on cereal production in many areas, and the frequency of drought is likely to increase in most arid and semi-arid regions under future climate change scenarios. Considerable research and breeding efforts have been devoted to investigating crop responses to drought at various levels and producing drought-resistant genotypes. Plant physiology has provided new insights to yield improvement in drought-prone environments. Crop performance could be improved through increases in water use, water-use efficiency (WUE) and harvest index. Greater WUE can be achieved by coordination between photosynthesis and transpiration. Carbon isotope discrimination (Δ(13) C) has been demonstrated to be a simple but reliable measure of WUE, and negative correlation between them has been used to indirectly estimate WUE under selected environments. New tools, such as quantitative trait loci (QTL) mapping and gene expression profiling, are playing vital roles in dissecting drought resistance-related traits. The combination of gene expression and association mapping could help identify candidate genes underlying the QTL of interest and complement map-based cloning and marker-assisted selection. Eventually, improved cultivars can be produced through genetic engineering. Future efficient and effective breeding progress in cereals under targeted drought environments will come from the integrated knowledge of physiology and genomics.
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Affiliation(s)
- Jing Chen
- Department of Renewable Resources, 442 Earth Sciences Building, University of Alberta, Edmonton, Alberta, Canada
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Miura K, Ashikari M, Matsuoka M. The role of QTLs in the breeding of high-yielding rice. TRENDS IN PLANT SCIENCE 2011; 16:319-26. [PMID: 21429786 DOI: 10.1016/j.tplants.2011.02.009] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Revised: 02/09/2011] [Accepted: 02/22/2011] [Indexed: 05/19/2023]
Abstract
Food shortages have once again become a serious problem, not only because of world population growth but also as a result of escalating demand for crops as a substrate for biofuels. The production of improved plant varieties, especially major crops such as rice, is urgently required to increase yield. The completion of the sequencing of the rice genome has made it possible to clone and analyze quantitative trait loci (QTLs). Furthermore, the development of high-throughput sequencing and genotyping technologies has improved spectacularly the accuracy of QTL analysis. In this review article, we focus on the potential roles of major QTLs in the selection for agronomic traits in rice and discuss the application of high-throughput technologies for high-resolution genetic analysis.
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Affiliation(s)
- Kotaro Miura
- Department of Bioscience, Fukui Prefectural University, 4-1-1 Matsuoka Kenjyojima, Eiheiji-cho, Yoshida-gun, Fukui, 910-1195, Japan
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125
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An analysis of the polymorphisms in a gene for being involved in drought tolerance in maize. Genetica 2011; 139:479-87. [DOI: 10.1007/s10709-011-9568-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Accepted: 03/15/2011] [Indexed: 10/18/2022]
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126
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Yan J, Warburton M, Crouch J. Association Mapping for Enhancing Maize ( Zea maysL.) Genetic Improvement. CROP SCIENCE 2011; 51:433-449. [PMID: 0 DOI: 10.2135/cropsci2010.04.0233] [Citation(s) in RCA: 181] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Affiliation(s)
- Jianbing Yan
- National Maize Improvement Center of China; China Agricultural Univ.; Beijing 100193 China
- International Maize and Wheat Improvement Center (CIMMYT); Apartado Postal 6-640 06600 Mexico DF Mexico
| | - Marilyn Warburton
- USDA-ARS; Corn Host Plant Resistance Research Unit; Box 9555 Mississippi State MS 39762
| | - Jonathan Crouch
- International Maize and Wheat Improvement Center (CIMMYT); Apartado Postal 6-640 06600 Mexico DF Mexico
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