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Wang P, Ma M, Chen H, Sun H, Wu D, He Q, Jing D, Guo Q, Dang J, Liang G. Global analysis of gene expression in response to double trisomy loquat (Eriobotrya japonica). Genomics 2024; 116:110913. [PMID: 39151554 DOI: 10.1016/j.ygeno.2024.110913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 08/02/2024] [Accepted: 08/07/2024] [Indexed: 08/19/2024]
Abstract
Aneuploidy generally has severe phenotypic consequences. However, the molecular basis for this has been focused on single chromosomal dosage changes. It is not clear how the karyotype of complex aneuploidies affects gene expression. Here, we identified six different double-trisomy loquat strains from Q24 progenies of triploid loquat. The differences and similarities of the transcriptional responses of different double trisomy loquat strains were studied systematically via RNA-seq. The global modulation of gene expression indicated that both cis and trans-effects coordinately regulated gene expression in aneuploid loquat to some extent, and this coordinated regulation was determined by different gene functional groups. Aneuploidy can induce specific transcriptional responses on loquat chromosomes. The differentially expressed genes exhibited regional gene expression dysregulation domains along chromosomes. Furthermore, Aneuploidy could also promote the expression of genes with moderate and high in loquats. Our results provide new insights into the genome-wide transcriptional effects of karyotypes with complex aneuploidies.
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Affiliation(s)
- Peng Wang
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education); College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China; Academy of Agricultural Sciences of Southwest University; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Miao Ma
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education); College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China; Academy of Agricultural Sciences of Southwest University; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Haichun Chen
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education); College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China; Academy of Agricultural Sciences of Southwest University; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Haiyan Sun
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education); College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China; Academy of Agricultural Sciences of Southwest University; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Di Wu
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education); College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China; Academy of Agricultural Sciences of Southwest University; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Qiao He
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education); College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China; Academy of Agricultural Sciences of Southwest University; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Danlong Jing
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education); College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China; Academy of Agricultural Sciences of Southwest University; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Qigao Guo
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education); College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China; Academy of Agricultural Sciences of Southwest University; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China.
| | - Jiangbo Dang
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education); College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China; Academy of Agricultural Sciences of Southwest University; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China.
| | - Guolu Liang
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education); College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China; Academy of Agricultural Sciences of Southwest University; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China.
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Sun S, Liu K, Xue C, Hu Y, Yu H, Qi G, Chen J, Li X, Zhao X, Gong Z. Genome-Wide Effects on Gene Expression Between Parental and Filial Generations of Trisomy 11 and 12 of Rice. RICE (NEW YORK, N.Y.) 2023; 16:17. [PMID: 36964817 PMCID: PMC10039966 DOI: 10.1186/s12284-023-00632-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/08/2023] [Indexed: 06/18/2023]
Abstract
Aneuploid refers to the gene dosage imbalance due to copy number alterations. Aneuploidy is generally harmful to the growth, development and reproduction of organisms according to the numerous research. However, it has rarely been reported on whether aneuploid have a relevant pattern of genome expression between the parental and its offspring generations. In this study, mRNA sequencing analysis was performed on rice (Oryza sativa L.) primary trisomes 11 and 12, same primary trisomes and normal individuals in their filial generation. We systematically summarized the changes in gene expression patterns that occur on cis genes and on trans genes between parental and filial generations. In T11 and T12, the ratio of cis-gene expression showed intermediate type in parents and dosage compensation in filial generations, which maybe due to more genes being downregulated. The trans genes were also affected by aneuploidy and manifested as cis-related. The strains with normal chromosomes in filial generations, there are still aneuploid-sensitive genes differentially expressed in their genomes, indicating that the effect of aneuploidy is far-reaching and could not be easily eliminated. Meanwhile, among these differentially expressed genes, genes with low-expression level were more likely to be upregulated, while genes with medium- and high-expression level were easy to be downregulated. For the different types of rice aneuploid, upregulated genes were mainly associated with genomic imbalance while downregulated genes were mainly influenced by the specific added chromosome. In conclusion, our results provide new insights into the genetic characterization and evolution of biological aneuploidy genomes.
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Affiliation(s)
- Shang Sun
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Kai Liu
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Chao Xue
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Yingying Hu
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Hengxiu Yu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Guoxiao Qi
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Jijin Chen
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Xiya Li
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Xinru Zhao
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Zhiyun Gong
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China.
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Martínez-Fortún J, Phillips DW, Jones HD. Natural and artificial sources of genetic variation used in crop breeding: A baseline comparator for genome editing. Front Genome Ed 2022; 4:937853. [PMID: 36072906 PMCID: PMC9441798 DOI: 10.3389/fgeed.2022.937853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
Traditional breeding has successfully selected beneficial traits for food, feed, and fibre crops over the last several thousand years. The last century has seen significant technological advancements particularly in marker assisted selection and the generation of induced genetic variation, including over the last few decades, through mutation breeding, genetic modification, and genome editing. While regulatory frameworks for traditional varietal development and for genetic modification with transgenes are broadly established, those for genome editing are lacking or are still evolving in many regions. In particular, the lack of "foreign" recombinant DNA in genome edited plants and that the resulting SNPs or INDELs are indistinguishable from those seen in traditional breeding has challenged development of new legislation. Where products of genome editing and other novel breeding technologies possess no transgenes and could have been generated via traditional methods, we argue that it is logical and proportionate to apply equivalent legislative oversight that already exists for traditional breeding and novel foods. This review analyses the types and the scale of spontaneous and induced genetic variation that can be selected during traditional plant breeding activities. It provides a base line from which to judge whether genetic changes brought about by techniques of genome editing or other reverse genetic methods are indeed comparable to those routinely found using traditional methods of plant breeding.
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Affiliation(s)
| | | | - Huw D. Jones
- IBERS, Aberystwyth University, Aberystwyth, United Kingdom
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Abstract
Aneuploidy, a genomic alternation characterized by deviations in the copy number of chromosomes, affects organisms from early development through to aging. Although it is a main cause of human pregnancy loss and a hallmark of cancer, how aneuploidy affects cellular function has been elusive. The last two decades have seen rapid advances in the understanding of the causes and consequences of aneuploidy at the molecular and cellular levels. These studies have uncovered effects of aneuploidy that can be beneficial or detrimental to cells and organisms in an environmental context-dependent and karyotype-dependent manner. Aneuploidy also imposes general stress on cells that stems from an imbalanced genome and, consequently, also an imbalanced proteome. These insights provide the fundamental framework for understanding the impact of aneuploidy in genome evolution, human pathogenesis and drug resistance.
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Shao Y, Pan Q, Zhang D, Kang L, Li Z. Global gene expression perturbations in rapeseed due to the introduction of alien radish chromosomes. J Genet 2021. [DOI: 10.1007/s12041-021-01276-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Algwaiz HI. Cytological Effect of Gamma Radiation on Selected Mutants of Wheat <i>Triticum aestivum</i> L. in M3 Generation. Pak J Biol Sci 2020; 22:607-613. [PMID: 31930860 DOI: 10.3923/pjbs.2019.607.613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND AND OBJECTIVE Wheat (Triticum aestivum L.) offers some unique opportunities for the induction and exploitation of agronomic value. The use of gamma radiation has been proven to be an effective method to induce genetic variation in crops. We aimed to determine genetically stable mutants of wheat which could be utilized for breeding purposes. MATERIALS AND METHODS We did a cytological investigation of induced mutant's behavior and chiasma frequency. Selected mutant types induced in dry and soaked seeds were treated with different doses of gamma rays. Each treated sample and control were subjected to cytological examination of the fixed pollen mother cells in various meiotic stages. RESULTS The percentage of the total abnormal cells significantly increased in one mutant and significantly decreased in the other mutant. The percentage of total abnormal cells did not diminish from the first to the second meiotic division. The types of meiotic anomalies found included laggards (56.51%), univalent (9.43%), stickiness (45.45%) and bridges (19.32%). There were genotypic differences in the frequency of occurrence of multivalent (trivalent and quadrivalents). A marked reduction in the number of rod and ring bivalent/cell in some genotypes were noticed. The frequency of chiasmata per pollen mother cell was reduced subsequently. Depression index of mutants was negative compared with controls or treatments except for a few genotypes. CONCLUSION Selected mutants of wheat tend to be cytologically stable and can therefore, be utilized for breeding purposes.
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Complex relationship between DNA methylation and gene expression due to Lr28 in wheat-leaf rust pathosystem. Mol Biol Rep 2019; 47:1339-1360. [DOI: 10.1007/s11033-019-05236-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 11/08/2019] [Accepted: 12/07/2019] [Indexed: 11/26/2022]
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Cara N, Ferrer MS, Masuelli RW, Camadro EL, Marfil CF. Epigenetic consequences of interploidal hybridisation in synthetic and natural interspecific potato hybrids. THE NEW PHYTOLOGIST 2019; 222:1981-1993. [PMID: 30681145 DOI: 10.1111/nph.15706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 01/17/2019] [Indexed: 06/09/2023]
Abstract
Interploidal hybridisation can generate changes in plant chromosome numbers, which might exert effects additional to the expected due to genome merger per se (that is genetic, epigenetic and phenotypic novelties). Wild potatoes are suitable to address this question in an evolutionary context. To this end, we performed genetic (AFLP and single sequence repeart (SSR)), epigenetic (MSAP), and cytological comparisons in: (1) natural populations of the diploid cytotype of the hybrid taxonomic species Solanum × rechei (2n = 2×, 3×) and its parental species, the triploid cytotype of Solanum microdontum (2n = 2×, 3×) and Solanum kurtzianum (2n = 2×); and (2) newly synthesised intraploidal (2× × 2×) and interploidal (3× × 2×) S. microdontum × S. kurtzianum hybrids. Aneuploidy was detected in S. × rechei and the synthetic interploidal progeny; this phenomenon might have originated the significantly higher number of methylation changes observed in the interploidal vs the intraploidal hybrids. The wide epigenetic variability induced by interploidal hybridisation is consistent with the novel epigenetic pattern established in S. × rechei compared to its parental species in nature. These results suggest that aneuploid potato lineages can persist throughout the short term, and possibly medium term, and that differences in parental ploidy resulting in aneuploidy are an additional source of epigenetic variation.
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Affiliation(s)
- Nicolás Cara
- Instituto de Biología Agrícola de Mendoza (IBAM), Facultad de Ciencias Agrarias, U.N.Cuyo, CONICET, Mendoza, Argentina
| | - María Soledad Ferrer
- Instituto de Biología Agrícola de Mendoza (IBAM), Facultad de Ciencias Agrarias, U.N.Cuyo, CONICET, Mendoza, Argentina
| | - Ricardo Williams Masuelli
- Instituto de Biología Agrícola de Mendoza (IBAM), Facultad de Ciencias Agrarias, U.N.Cuyo, CONICET, Mendoza, Argentina
| | - Elsa Lucila Camadro
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, CONICET, Mar del Plata, Argentina
| | - Carlos Federico Marfil
- Instituto de Biología Agrícola de Mendoza (IBAM), Facultad de Ciencias Agrarias, U.N.Cuyo, CONICET, Mendoza, Argentina
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Wang M, Ji Y, Feng S, Liu C, Xiao Z, Wang X, Wang Y, Xia G. The non-random patterns of genetic variation induced by asymmetric somatic hybridization in wheat. BMC PLANT BIOLOGY 2018; 18:244. [PMID: 30332989 PMCID: PMC6192298 DOI: 10.1186/s12870-018-1474-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/05/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Asymmetric somatic hybridization is an efficient crop breeding approach by introducing several exogenous chromatin fragments, which leads to genomic shock and therefore induces genome-wide genetic variation. However, the fundamental question concerning the genetic variation such as whether it occurs randomly and suffers from selection pressure remains unknown. RESULTS Here, we explored this issue by comparing expressed sequence tags of a common wheat cultivar and its asymmetric somatic hybrid line. Both nucleotide substitutions and indels (insertions and deletions) had lower frequencies in coding sequences than in un-translated regions. The frequencies of nucleotide substitutions and indels were both comparable between chromosomes with and without introgressed fragments. Nucleotide substitutions distributed unevenly and were preferential to indel-flanking sequences, and the frequency of nucleotide substitutions at 5'-flanking sequences of indels was obviously higher in chromosomes with introgressed fragments than in those without exogenous fragment. Nucleotide substitutions and indels both had various frequencies among seven groups of allelic chromosomes, and the frequencies of nucleotide substitutions were strongly negatively correlative to those of indels. Among three sets of genomes, the frequencies of nucleotide substitutions and indels were both heterogeneous, and the frequencies of nucleotide substitutions exhibited drastically positive correlation to those of indels. CONCLUSIONS Our work demonstrates that the genetic variation induced by asymmetric somatic hybridization is attributed to both whole genomic shock and local chromosomal shock, which is a predetermined and non-random genetic event being closely associated with selection pressure. Asymmetric somatic hybrids provide a worthwhile model to further investigate the nature of genomic shock induced genetic variation.
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Affiliation(s)
- Mengcheng Wang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100 People’s Republic of China
| | - Yujie Ji
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shiting Feng
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100 People’s Republic of China
| | - Chun Liu
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100 People’s Republic of China
| | - Zhen Xiao
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100 People’s Republic of China
| | - Xiaoping Wang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100 People’s Republic of China
| | - Yanxia Wang
- Shijiazhuang Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050041 China
| | - Guangmin Xia
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100 People’s Republic of China
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Deng X, Sha Y, Lv Z, Wu Y, Zhang A, Wang F, Liu B. The Capacity to Buffer and Sustain Imbalanced D-Subgenome Chromosomes by the BBAA Component of Hexaploid Wheat Is an Evolved Dominant Trait. FRONTIERS IN PLANT SCIENCE 2018; 9:1149. [PMID: 30131821 PMCID: PMC6090280 DOI: 10.3389/fpls.2018.01149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 07/18/2018] [Indexed: 06/08/2023]
Abstract
Successful generation of pentaploid wheat (genome, BBAAD) via interspecific hybridization between tetraploid wheat (BBAA) and hexaploid wheat (BBAADD) holds great promise to mutually exchange desirable traits between the two cultivated wheat species, as well as providing a novel facet for evolutionary studies of polyploid wheat. Taking advantage of the viable and fertile nature of an extracted tetraploid wheat (ETW) with a BBAA genome that is virtually identical with the BBAA component of a hexaploid common wheat, and a synthetic hexaploid wheat, we constructed four pentaploid wheats with several distinct yet complementary features, of which harboring homozygous BBAA subgenomes is a common feature. By using a combined FISH/GISH method that enables diagnosing all individual wheat chromosomes, we precisely karyotyped a larger number of cohorts from the immediate progenies of each of the four pentaploid wheats. We found that the BBAA component of hexaploid common wheat possesses a significantly stronger capacity to buffer and sustain imbalanced D genome chromosomes and appears to harbor more structural chromosome variations than the BBAA genome of tetraploid wheat. We also document that this stronger capacity of the hexaploid BBAA subgenomes behaves as a genetically controlled dominant trait. Our findings bear implications to the known greater than expected level of genetic diversity in, and the remarkable adaptability of, hexaploid common wheat as a staple crop of global significance, as well as in using pentaploidy as intermediates for reciprocal introgression of useful traits between tetraploid and hexaploid wheat cultivars.
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Affiliation(s)
- Xin Deng
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Yan Sha
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Zhenling Lv
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Ying Wu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Ai Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Fang Wang
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
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Wu Y, Sun Y, Sun S, Li G, Wang J, Wang B, Lin X, Huang M, Gong Z, Sanguinet KA, Zhang Z, Liu B. Aneuploidization under segmental allotetraploidy in rice and its phenotypic manifestation. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1273-1285. [PMID: 29478186 PMCID: PMC5945760 DOI: 10.1007/s00122-018-3077-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 02/15/2018] [Indexed: 05/24/2023]
Abstract
We report a repertoire of diverse aneuploids harbored by a newly synthesized segmental allotetraploid rice population with fully sequenced sub-genomes and demonstrate their retention features and phenotypic consequences. Aneuploidy, defined as unequal numbers of different chromosomes, is a large-effect genetic variant and may produce diverse cellular and organismal phenotypes. Polyploids are more permissive to chromosomal content imbalance than their diploid and haploid counterparts, and therefore, may enable more in-depth investigation of the phenotypic consequences of aneuploidy. Based on whole-genome resequencing, we identify that ca. 40% of the 312 selfed individual plants sampled from an early generation rice segmental allotetraploid population are constitutive aneuploids harboring 55 distinct aneuploid karyotypes. We document that gain of a chromosome is more prevalent than loss of a chromosome, and the 12 rice chromosomes have distinct tendencies to be in an aneuploid state. These properties of aneuploidy are constrained by multiple factors including the number of genes residing on the chromosome and predicted functional connectivity with other chromosomes. Two broad categories of aneuploidy-associated phenotypes are recognized: those shared by different aneuploids, and those associated with aneuploidy of a specific chromosome. A repertoire of diverse aneuploids in the context of a segmental allotetraploid rice genome with fully sequenced sub-genomes provides a tractable resource to explore the roles of aneuploidy in nascent polyploid genome evolution and helps to decipher the mechanisms conferring karyotypic stabilization on the path to polyploid speciation and towards artificial construction of novel polyploid crops.
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Affiliation(s)
- Ying Wu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Yue Sun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Shuai Sun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Guo Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Jie Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bin Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Xiuyun Lin
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Meng Huang
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Zhiyun Gong
- Agricultural College, Yangzhou University, Yangzhou, 225009, China
| | - Karen A Sanguinet
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Zhiwu Zhang
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
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Liu C, Wang M, Wang L, Guo Q, Liang G. Extensive genetic and DNA methylation variation contribute to heterosis in triploid loquat hybrids. Genome 2018; 61:437-447. [PMID: 29687741 DOI: 10.1139/gen-2017-0232] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We aim to overcome the unclear origin of the loquat and elucidate the heterosis mechanism of the triploid loquat. Here we investigated the genetic and epigenetic variations between the triploid plant and its parental lines using amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified fragment length polymorphism (MSAP) analyses. We show that in addition to genetic variations, extensive DNA methylation variation occurred during the formation process of triploid loquat, with the triploid hybrid having increased DNA methylation compared to the parents. Furthermore, a correlation existed between genetic variation and DNA methylation remodeling, suggesting that genome instability may lead to DNA methylation variation or vice versa. Sequence analysis of the MSAP bands revealed that over 53% of them overlap with protein-coding genes, which may indicate a functional role of the differential DNA methylation in gene regulation and hence heterosis phenotypes. Consistent with this, the genetic and epigenetic alterations were associated closely to the heterosis phenotypes of triploid loquat, and this association varied for different traits. Our results suggested that the formation of triploid is accompanied by extensive genetic and DNA methylation variation, and these changes contribute to the heterosis phenotypes of the triploid loquats from the two cross lines.
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Affiliation(s)
- Chao Liu
- a Key Laboratory of Horticulture Science for Southern Mountainous Region, Ministry of Education/College of Horticulture and Landscape Architecture, Southwest University, Tiansheng Road 2, 400715, Chongqing, P.R. China
| | - Mingbo Wang
- b CSIRO Agriculture and Food, Clunies Ross Street, Canberra ACT 2061, Australia
| | - Lingli Wang
- c Technical Advice Station of Economic Crop, Yubei district, Chongqing, P.R. China
| | - Qigao Guo
- a Key Laboratory of Horticulture Science for Southern Mountainous Region, Ministry of Education/College of Horticulture and Landscape Architecture, Southwest University, Tiansheng Road 2, 400715, Chongqing, P.R. China
| | - Guolu Liang
- a Key Laboratory of Horticulture Science for Southern Mountainous Region, Ministry of Education/College of Horticulture and Landscape Architecture, Southwest University, Tiansheng Road 2, 400715, Chongqing, P.R. China
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Ding M, Chen ZJ. Epigenetic perspectives on the evolution and domestication of polyploid plant and crops. CURRENT OPINION IN PLANT BIOLOGY 2018; 42:37-48. [PMID: 29502038 PMCID: PMC6058195 DOI: 10.1016/j.pbi.2018.02.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 02/07/2018] [Accepted: 02/13/2018] [Indexed: 05/19/2023]
Abstract
Polyploidy or whole genome duplication (WGD) is a prominent feature for genome evolution of some animals and all flowering plants, including many important crops such as wheat, cotton, and canola. In autopolyploids, genome duplication often perturbs dosage regulation on biological networks. In allopolyploids, interspecific hybridization could induce genetic and epigenetic changes, the effects of which could be amplified by genome doubling (ploidy changes). Albeit the importance of genetic changes, some epigenetic changes can be stabilized and transmitted as epialleles into the progeny, which are subject to natural selection, adaptation, and domestication. Here we review recent advances for general and specific roles of epigenetic changes in the evolution of flowering plants and domestication of agricultural crops.
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Affiliation(s)
- Mingquan Ding
- Departments of Molecular Biosciences and Integrative Biology, Institute for Cellular and Molecular Biology, and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA
| | - Z Jeffrey Chen
- Departments of Molecular Biosciences and Integrative Biology, Institute for Cellular and Molecular Biology, and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA; State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
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14
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Yang M, Gao X, Dong J, Gandhi N, Cai H, von Wettstein DH, Rustgi S, Wen S. Pattern of Protein Expression in Developing Wheat Grains Identified through Proteomic Analysis. FRONTIERS IN PLANT SCIENCE 2017; 8:962. [PMID: 28649254 PMCID: PMC5465268 DOI: 10.3389/fpls.2017.00962] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 05/22/2017] [Indexed: 05/20/2023]
Abstract
Grain development is one of the biological processes, which contributes to the final grain yield. To understand the molecular changes taking place during the early grain development, we profiled proteomes of two common wheat cultivars P271 and Chinese Spring (CS) with large and small grains, respectively at three grain developmental stages (4, 8, and 12 days post anthesis). An iTRAQ (isobaric tags for relative and absolute quantitation) based proteomics approach was used for this purpose. More than 3,600 proteins were reported to accumulate during early grain development in both wheat cultivars. Of these 3,600 proteins, 130 expressed differentially between two wheat cultivars, and 306 exhibited developmental stage-specific accumulation in either or both genotypes. Detailed bioinformatic analyses of differentially expressed proteins (DEPs) from the large- and small-grain wheat cultivars underscored the developmental differences observed between them and shed light on the molecular and cellular processes contributing to these differences. In silico localization of either or both sets of DEPs to wheat chromosomes exhibited a biased genomic distribution with chromosome 4D contributing largely to it. These results corresponded well with the earlier studies, performed in common wheat, where chromosome 4D was reported to harbor QTLs for yield contributing traits specifically grain length. Collectively, our results provide insight into the molecular processes taking place during early grain development, a knowledge, which may prove useful in improving wheat grain yield in the future.
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Affiliation(s)
- Mingming Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
- Wheat Engineering Research Center of Shaanxi Province, Northwest A&F UniversityYangling, China
| | - Xiang Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
- Wheat Engineering Research Center of Shaanxi Province, Northwest A&F UniversityYangling, China
- *Correspondence: Xiang Gao
| | - Jian Dong
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
- Wheat Engineering Research Center of Shaanxi Province, Northwest A&F UniversityYangling, China
| | - Nitant Gandhi
- Department of Plant and Environmental Sciences, Clemson University Pee Dee Research and Education CenterFlorence, SC, United States
| | - Huanjie Cai
- Key Laboratory of Agricultural Soil and Water Engineering in Arid and Semiarid Areas, Ministry of Education, Northwest A&F UniversityYangling, China
- Institute of Water Saving Agriculture in Arid Regions of China, Northwest A&F UniversityYangling, China
| | - Diter H. von Wettstein
- Department of Crop and Soil Sciences, Washington State UniversityPullman, WA, United States
| | - Sachin Rustgi
- Department of Plant and Environmental Sciences, Clemson University Pee Dee Research and Education CenterFlorence, SC, United States
- Department of Crop and Soil Sciences, Washington State UniversityPullman, WA, United States
- Sachin Rustgi
| | - Shanshan Wen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
- Shanshan Wen
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