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Mertten D, Baldwin S, Cheng CH, McCallum J, Thomson S, Ashton DT, McKenzie CM, Lenhard M, Datson PM. Implementation of different relationship estimate methodologies in breeding value prediction in kiwiberry ( Actinidia arguta). Mol Breed 2023; 43:75. [PMID: 37868140 PMCID: PMC10584781 DOI: 10.1007/s11032-023-01419-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 10/02/2023] [Indexed: 10/24/2023]
Abstract
In dioecious crops such as Actinidia arguta (kiwiberries), some of the main challenges when breeding for fruit characteristics are the selection of potential male parents and the long juvenile period. Currently, breeding values of male parents are estimated through progeny tests, which makes the breeding of new kiwiberry cultivars time-consuming and costly. The application of best linear unbiased prediction (BLUP) would allow direct estimation of sex-related traits and speed up kiwiberry breeding. In this study, we used a linear mixed model approach to estimate narrow sense heritability for one vine-related trait and five fruit-related traits for two incomplete factorial crossing designs. We obtained BLUPs for all genotypes, taking into consideration whether the relationship was pedigree-based or marker-based. Owing to the high cost of genome sequencing, it is important to understand the effects of different sources of relationship matrices on estimating breeding values across a breeding population. Because of the increasing implementation of genomic selection in crop breeding, we compared the effects of incorporating different sources of information in building relationship matrices and ploidy levels on the accuracy of BLUPs' heritability and predictive ability. As kiwiberries are autotetraploids, multivalent chromosome formation and occasionally double reduction can occur during meiosis, and this can affect the accuracy of prediction. This study innovates the breeding programme of autotetraploid kiwiberries. We demonstrate that the accuracy of BLUPs of male siblings, without phenotypic observations, strongly improved when a tetraploid marker-based relationship matrix was used rather than parental BLUPs and female siblings with phenotypic observations. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01419-8.
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Affiliation(s)
- Daniel Mertten
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Auckland, 1142 New Zealand
- Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam-Golm, Germany
| | | | | | | | | | | | | | - Michael Lenhard
- Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam-Golm, Germany
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Bomblies K. Learning to tango with four (or more): the molecular basis of adaptation to polyploid meiosis. Plant Reprod 2023; 36:107-124. [PMID: 36149479 PMCID: PMC9957869 DOI: 10.1007/s00497-022-00448-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/10/2022] [Indexed: 05/29/2023]
Abstract
Polyploidy, which arises from genome duplication, has occurred throughout the history of eukaryotes, though it is especially common in plants. The resulting increased size, heterozygosity, and complexity of the genome can be an evolutionary opportunity, facilitating diversification, adaptation and the evolution of functional novelty. On the other hand, when they first arise, polyploids face a number of challenges, one of the biggest being the meiotic pairing, recombination and segregation of the suddenly more than two copies of each chromosome, which can limit their fertility. Both for developing polyploidy as a crop improvement tool (which holds great promise due to the high and lasting multi-stress resilience of polyploids), as well as for our basic understanding of meiosis and plant evolution, we need to know both the specific nature of the challenges polyploids face, as well as how they can be overcome in evolution. In recent years there has been a dramatic uptick in our understanding of the molecular basis of polyploid adaptations to meiotic challenges, and that is the focus of this review.
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Affiliation(s)
- Kirsten Bomblies
- Plant Evolutionary Genetics, Institute of Plant Molecular Biology, Department of Biology, ETH Zürich, Zurich, Switzerland.
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Scarrow M, Chen N, Namaganda A, Sun G. N 6-Methyladenosine and physiological response divergence confer autotetraploid enhanced salt tolerance compared to its diploid Hordeum bulbosum. Physiol Mol Biol Plants 2022; 28:2013-2021. [PMID: 36573150 PMCID: PMC9789291 DOI: 10.1007/s12298-022-01260-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Polyploid species have played an essential role in plant evolution, exemplified by adaptive advantages to abiotic stress. N 6-Methyladenosine (m6A) is suggested to play an important role in stress response. However, whether genome doubling affects m6A to increase autopolyploids stress tolerance is still unclear. This study aims to compare physiological (maintaining osmoregulatory homeostasis) and m6A changes between autotetraploid and diploid wild barley (Hordeum bulbosum) in response to salt (NaCl) stress. Results showed that autotetraploids physiologically had enhanced stress tolerance based on the measured parameters of relative water content, water loss, proline, H2O2, and chlorophyll. Diploid H. bulbosum experienced an excessive abundance of proline following salt stress where tetraploids had beneficial proline accumulation and thus enhanced osmoregulation. The significantly higher level of proline and H2O2 in diploid than in autotetraploid implies that diploids suffered higher osmotic stress than autotetraploid. Autotetraploid produced enough proline to protect stress, but not so much to cause toxicity. m6A in total RNA showed no significant difference between ploidies in controls, but was significantly higher in autotetraploids than in diploids during stress and recovery. These results suggest that increased m6A might be one of molecular mechanisms that increases salt tolerance in autotetraploid H. bulbosum compared to diploids, which enhances the adaptation of autopolyploids. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-022-01260-x.
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Affiliation(s)
| | - Ning Chen
- Biology Department, Saint Mary’s University, Halifax, NS Canada
| | | | - Genlou Sun
- Biology Department, Saint Mary’s University, Halifax, NS Canada
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Zhou C, Liu X, Li X, Zhou H, Wang S, Yuan Z, Zhang Y, Li S, You A, Zhou L, He Z. A Genome Doubling Event Reshapes Rice Morphology and Products by Modulating Chromatin Signatures and Gene Expression Profiling. Rice (N Y) 2021; 14:72. [PMID: 34347189 PMCID: PMC8339180 DOI: 10.1186/s12284-021-00515-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/27/2021] [Indexed: 05/16/2023]
Abstract
Evolutionarily, polyploidy represents a smart method for adjusting agronomically important in crops through impacts on genomic abundance and chromatin condensation. Autopolyploids have a relatively concise genetic background with great diversity and provide an ideal system to understand genetic and epigenetic mechanisms attributed to the genome-dosage effect. However, whether and how genome duplication events during autopolyploidization impact chromatin signatures are less understood in crops. To address it, we generated an autotetraploid rice line from a diploid progenitor, Oryza sativa ssp. indica 93-11. Using transposase-accessible chromatin sequencing, we found that autopolyploids lead to a higher number of accessible chromatin regions (ACRs) in euchromatin, most of which encode protein-coding genes. As expected, the profiling of ACR densities supported that the effect of ACRs on transcriptional gene activities relies on their positions in the rice genome, regardless of genome doubling. However, we noticed that genome duplication favors genic ACRs as the main drivers of transcriptional changes. In addition, we probed intricate crosstalk among various kinds of epigenetic marks and expression patterns of ACR-associated gene expression in both diploid and autotetraploid rice plants by integrating multiple-omics analyses, including chromatin immunoprecipitation sequencing and RNA-seq. Our data suggested that the combination of H3K36me2 and H3K36me3 may be associated with dynamic perturbation of ACRs introduced by autopolyploidization. As a consequence, we found that numerous metabolites were stimulated by genome doubling. Collectively, our findings suggest that autotetraploids reshape rice morphology and products by modulating chromatin signatures and transcriptional profiling, resulting in a pragmatic means of crop genetic improvement.
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Affiliation(s)
- Chao Zhou
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang, 443002, China.
| | - Xiaoyun Liu
- Institute for Interdisciplinary Research, Jianghan University, Wuhan, 430056, China
| | - Xinglei Li
- Bioacme Biotechnology Co., Ltd., Wuhan, 430056, China
| | - Hanlin Zhou
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang, 443002, China
| | - Sijia Wang
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang, 443002, China
| | - Zhu Yuan
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang, 443002, China
| | - Yonghong Zhang
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan, 442000, China
| | - Sanhe Li
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Aiqing You
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Lei Zhou
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China.
| | - Zhengquan He
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang, 443002, China.
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Cara N, Piccoli PN, Bolcato L, Marfil CF, Masuelli RW. Variation in the amino acids, volatile organic compounds and terpenes profiles in induced polyploids and in Solanum tuberosum varieties. Phytochemistry 2020; 180:112516. [PMID: 32949937 DOI: 10.1016/j.phytochem.2020.112516] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 07/25/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
Polyploids often display a variety of phenotypic novelties when compared to their diploid progenitors, some of which may represent ecological advantages, especially regarding tolerance to biotic and abiotic factors. Plants cope with environmental factors by producing chemicals such as volatile organic compounds (VOCs) and specific amino acids (AAs). In potato, the third most important food crop in the world, gene introgression from diploid wild relative species into the genetic pool of the cultivated species (tetraploid) would be of great agronomical interest. The consequences of allopolyploidization on the potato VOCs and AAs profiles have not been yet analyzed. In this work, the effects of whole genome duplication on VOCs and AAs contents in leaves of potato allo- and autotetraploids and cultivated varieties were studied. The polyploids were obtained by chromosomal duplication of a genotype of the wild diploid species S. kurtzianum (autopolyploid model), and a diploid interspecific hybrid between the cultivated species S. tuberosum and S. kurtzianum (allopolyploid model). Almost all compounds levels varied greatly among these tetraploid lines; while all tetraploids showed higher contents of non-isoprenoids compounds than diploids, we found either increments or reductions in terpenes and AAs content. The results support the idea that genome duplication is a stochastic source of variability, which might be directly used for introgression in the 4x gene pool of the cultivated potato by sexual hybridization.
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Affiliation(s)
- Nicolás Cara
- Facultad de Ciencias Agrarias, UNCuyo, Almirante Brown 500, M5528AHB, Mendoza, Argentina.
| | - Patricia N Piccoli
- Facultad de Ciencias Agrarias, UNCuyo, Almirante Brown 500, M5528AHB, Mendoza, Argentina; Instituto de Biología Agrícola de Mendoza (IBAM), CONICET-UNCuyo, Almirante Brown 500, M5528AHB, Mendoza, Argentina.
| | - Leonardo Bolcato
- Instituto de Biología Agrícola de Mendoza (IBAM), CONICET-UNCuyo, Almirante Brown 500, M5528AHB, Mendoza, Argentina.
| | - Carlos F Marfil
- Facultad de Ciencias Agrarias, UNCuyo, Almirante Brown 500, M5528AHB, Mendoza, Argentina; Instituto de Biología Agrícola de Mendoza (IBAM), CONICET-UNCuyo, Almirante Brown 500, M5528AHB, Mendoza, Argentina.
| | - Ricardo W Masuelli
- Facultad de Ciencias Agrarias, UNCuyo, Almirante Brown 500, M5528AHB, Mendoza, Argentina; Instituto de Biología Agrícola de Mendoza (IBAM), CONICET-UNCuyo, Almirante Brown 500, M5528AHB, Mendoza, Argentina.
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Yamamoto E, Shirasawa K, Kimura T, Monden Y, Tanaka M, Isobe S. Genetic Mapping in Autohexaploid Sweet Potato with Low-Coverage NGS-Based Genotyping Data. G3 (Bethesda) 2020; 10:2661-70. [PMID: 32482727 DOI: 10.1534/g3.120.401433] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Next-generation sequencing (NGS)-based genotyping methods can generate numerous genetic markers in a single experiment and have contributed to plant genetic mapping. However, for high precision genetic analysis, the complicated genetic segregation mode in polyploid organisms requires high-coverage NGS data and elaborate analytical algorithms. In the present study, we propose a simple strategy for the genetic mapping of polyploids using low-coverage NGS data. The validity of the strategy was investigated using simulated data. Previous studies indicated that accurate allele dosage estimation from low-coverage NGS data (read depth < 40) is difficult. Therefore, we used allele dosage probabilities calculated from read counts in association analyses to detect loci associated with phenotypic variations. The allele dosage probabilities showed significant detection power, although higher allele dosage estimation accuracy resulted in higher detection power. On the contrary, differences in the segregation patterns between the marker and causal genes resulted in a drastic decrease in detection power even if the marker and casual genes were in complete linkage and the allele dosage estimation was accurate. These results indicated that the use of a larger number of markers is advantageous, even if the accuracy of allele dosage estimation is low. Finally, we applied the strategy for the genetic mapping of autohexaploid sweet potato (Ipomoea batatas) populations to detect loci associated with agronomic traits. Our strategy could constitute a cost-effective approach for preliminary experiments done performed to large-scale studies.
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Nakano M, Taniguchi K, Masuda Y, Kozuka T, Aruga Y, Han J, Motohara K, Nakata M, Sumitomo K, Hisamatsu T, Nakano Y, Yagi M, Hirakawa H, Isobe SN, Shirasawa K, Nagashima Y, Na H, Chen L, Liang G, Chen R, Kusaba M. A pure line derived from a self-compatible Chrysanthemum seticuspe mutant as a model strain in the genus Chrysanthemum. Plant Sci 2019; 287:110174. [PMID: 31481216 DOI: 10.1016/j.plantsci.2019.110174] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/19/2019] [Accepted: 06/21/2019] [Indexed: 06/10/2023]
Abstract
Asteraceae is the largest family of angiosperms, comprising approximately 24,000 species. Molecular genetic studies of Asteraceae are essential for understanding plant diversity. Chrysanthemum morifolium is the most industrially important ornamental species in Asteraceae. Most cultivars of C. morifolium are autohexaploid and self-incompatible. These properties are major obstacles to the genetic analysis and modern breeding of C. morifolium. Furthermore, high genome heterogeneity complicates molecular biological analyses. In this study, we developed a model strain in the genus Chrysanthemum. C. seticuspe is a diploid species with a similar flowering property and morphology to C. morifolium and can be subjected to Agrobacterium-mediated transformation. We isolated a natural self-compatible mutant of C. seticuspe and established a pure line through repeated selfing and selection. The resultant strain, named Gojo-0, was favorable for genetic analyses, including isolation of natural and induced mutants, and facilitated molecular biological analysis, including whole genome sequencing, owing to the simplicity and homogeneity of its genome. Interspecific hybridization with Chrysanthemum species was possible, enabling molecular genetic analysis of natural interspecific variations. The accumulation of research results and resources using Gojo-0 as a platform is expected to promote molecular genetic studies on the genus Chrysanthemum and the genetic improvement of chrysanthemum cultivars.
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Affiliation(s)
- Michiharu Nakano
- Graduate school of Integrated Sciences for Life, Hiroshima University, 1-4-3, Kagamiyama, Higashi-Hiroshima, 739-8526, Japan
| | - Kenji Taniguchi
- Graduate school of Integrated Sciences for Life, Hiroshima University, 1-4-3, Kagamiyama, Higashi-Hiroshima, 739-8526, Japan
| | - Yu Masuda
- Graduate school of Integrated Sciences for Life, Hiroshima University, 1-4-3, Kagamiyama, Higashi-Hiroshima, 739-8526, Japan
| | - Toshiaki Kozuka
- Graduate school of Integrated Sciences for Life, Hiroshima University, 1-4-3, Kagamiyama, Higashi-Hiroshima, 739-8526, Japan
| | - Yuki Aruga
- Graduate school of Integrated Sciences for Life, Hiroshima University, 1-4-3, Kagamiyama, Higashi-Hiroshima, 739-8526, Japan
| | - Jin Han
- Graduate school of Integrated Sciences for Life, Hiroshima University, 1-4-3, Kagamiyama, Higashi-Hiroshima, 739-8526, Japan
| | - Koichiro Motohara
- Graduate school of Integrated Sciences for Life, Hiroshima University, 1-4-3, Kagamiyama, Higashi-Hiroshima, 739-8526, Japan
| | - Masashi Nakata
- Botanic Gardens of Toyama, Kamikutsuwada 42, Fuchu-machi, Toyama, 939-2713, Japan
| | - Katsuhiko Sumitomo
- Institute of Vegetable and Floriculture Sciences, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki, 305-0852, Japan
| | - Tamotsu Hisamatsu
- Institute of Vegetable and Floriculture Sciences, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki, 305-0852, Japan
| | - Yoshihiro Nakano
- Institute of Vegetable and Floriculture Sciences, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki, 305-0852, Japan
| | - Masafumi Yagi
- Institute of Vegetable and Floriculture Sciences, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki, 305-0852, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, 292-0818, Japan
| | - Sachiko N Isobe
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, 292-0818, Japan
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, 292-0818, Japan
| | - Yumi Nagashima
- Graduate school of Integrated Sciences for Life, Hiroshima University, 1-4-3, Kagamiyama, Higashi-Hiroshima, 739-8526, Japan
| | - Haiyan Na
- College of Life Sciences, Sichuan University, Chengdu, 610064, Sichuan, China
| | - Li Chen
- College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Guolu Liang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Ruiyan Chen
- College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Makoto Kusaba
- Graduate school of Integrated Sciences for Life, Hiroshima University, 1-4-3, Kagamiyama, Higashi-Hiroshima, 739-8526, Japan.
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Yang Y, Wei F, Braynen J, Wei X, Tian B, Shi G, Cao G, Yuan J, Zhang X. Cytological and proteomic analyses of floral buds reveal an altered atlas of meiosis in autopolyploid Brassica rapa. Cell Biosci 2019; 9:49. [PMID: 31236208 PMCID: PMC6580506 DOI: 10.1186/s13578-019-0313-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 06/14/2019] [Indexed: 12/21/2022] Open
Abstract
Background Polyploidy is considered as a basic event in plant speciation and evolution in nature, and the cytological and proteomic profilings of floral buds at meiosis (FAM) would definitely contribute to a better understanding of the polyploid-associated effects during plant reproduction cycle. Results Herein, the cytological investigations demonstrated that chromosome behaviors such as univalent and multivalent at prophase I, chaotic alignments at metaphase, aberrant segregation at telophase, were frequently observed during meiosis in autotetraploid Brassica rapa. The proteomic analysis showed a total of 562 differentially expressed proteins (DEPs) were identified in FAM between autotetraploid and diploid B. rapa. Notably, PARP2 and LIG1 related to base excision repair and BARD1 involved in recombination were significantly down-regulated in autotetraploid B. rapa, which indicated DNA repair pathway were more likely affected during meiosis in autotetraploid B. rapa. The functional analysis showed that DEPs assigned to “chromatin structure and dynamics”, “cell cycle control, cell division, chromosome partitioning” and “cytoskeleton” were preferentially up-regulated, which suggested a robust regulation of cell division in autotetraploid B. rapa. In combination with the floral RNA-seq data released, a number of DEPs were found positively correlated with their transcript abundance, but posttranslational modification of proteins might also play a role in regulating meiosis course after polyploidization. Conclusions In general, this study provides a detailed cytology and proteome landscape of FAM between diploid and autotetraploid B. rapa, which definitely affords us a better understanding of uniformity and discrepancy of meiosis at the plant reproductive stage before and after polyploidization. Electronic supplementary material The online version of this article (10.1186/s13578-019-0313-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yan Yang
- 1School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China.,2School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China
| | - Fang Wei
- 1School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China.,2School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China
| | - Janeen Braynen
- 2School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China.,3Institute of Horticultural Research, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan People's Republic of China
| | - Xiaochun Wei
- 3Institute of Horticultural Research, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan People's Republic of China
| | - Baoming Tian
- 1School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China
| | - Gongyao Shi
- 1School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China
| | - Gangqiang Cao
- 1School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China
| | - Jiachen Yuan
- 2School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China
| | - Xiaowei Zhang
- 3Institute of Horticultural Research, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan People's Republic of China
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de Bem Oliveira I, Resende MFR Jr, Ferrão LFV, Amadeu RR, Endelman JB, Kirst M, Coelho ASG, Munoz PR. Genomic Prediction of Autotetraploids; Influence of Relationship Matrices, Allele Dosage, and Continuous Genotyping Calls in Phenotype Prediction. G3 (Bethesda) 2019; 9:1189-98. [PMID: 30782769 DOI: 10.1534/g3.119.400059] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Estimation of allele dosage, using genomic data, in autopolyploids is challenging and current methods often result in the misclassification of genotypes. Some progress has been made when using SNP arrays, but the major challenge is when using next generation sequencing data. Here we compare the use of read depth as continuous parameterization with ploidy parameterizations in the context of genomic selection (GS). Additionally, different sources of information to build relationship matrices were compared. A real breeding population of the autotetraploid species blueberry (Vaccinium corybosum), composed of 1,847 individuals was phenotyped for eight yield and fruit quality traits over two years. Continuous genotypic based models performed as well as the best models. This approach also reduces the computational time and avoids problems associated with misclassification of genotypic classes when assigning dosage in polyploid species. This approach could be very valuable for species with higher ploidy levels or for emerging crops where ploidy is not well understood. To our knowledge, this work constitutes the first study of genomic selection in blueberry. Accuracies are encouraging for application of GS for blueberry breeding. GS could reduce the time for cultivar release by three years, increasing the genetic gain per cycle by 86% on average when compared to phenotypic selection, and 32% when compared with pedigree-based selection. Finally, the genotypic and phenotypic data used in this study are made available for comparative analysis of dosage calling and genomic selection prediction models in the context of autopolyploids.
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Abstract
Andrographis paniculata (Burm. f.) Nees (AP) is commonly used for the treatment of many infectious diseases and has been cultivated widely in Asian countries, and has been included in United States Pharmacopoeia as a dietary supplement, but the cultivars of A. paniculata are not abundant due to its self-pollinated. With the aims to enrich AP resources and provide materials for after breeding we explored the polyploidy induction. Different explants, colchicine concentration, and treatment time were tested. After identification by flow cytometry, eleven polyploid plants with different morphologic traits were obtained. The agronomic traits and andrographolide concentration of the polyploids were improved greatly. One of the polyploids (serial 3-7) was chosen for further study. The traits of the second and third generation polyploids (serial 3-7) were stable. Compared with the normal plants, the seeds (2nd generation) weight increased by 31%, and the andrographolide concentration of the leaves increased by 14% (2nd) and 28% (3rd). In conclusion, AP autopolyploids with different morphologic traits were established successfully for the first time, and the polyploids induction might be effective for crop improvement of AP.
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Affiliation(s)
- Qi-Qing Li
- Institute of Biotechnology for TCM research, School of Traditional Chinese Medicine, China Pharmaceutical University, Nanjing 211198, China
| | - Jian Zhang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Ji-Hua Liu
- Institute of Biotechnology for TCM research, School of Traditional Chinese Medicine, China Pharmaceutical University, Nanjing 211198, China
| | - Bo-Yang Yu
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, China Pharmaceutical University, Nanjing 210009, China.
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