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Liu Q, Zhao Y, Rahman S, She M, Zhang J, Yang R, Islam S, O'Hara G, Varshney RK, Liu H, Ma H, Ma W. The putative vacuolar processing enzyme gene TaVPE3cB is a candidate gene for wheat stem pith-thickness. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:138. [PMID: 37233825 DOI: 10.1007/s00122-023-04372-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 04/27/2023] [Indexed: 05/27/2023]
Abstract
KEY MESSAGE The vacuolar processing enzyme gene TaVPE3cB is identified as a candidate gene for a QTL of wheat pith-thickness on chromosome 3B by BSR-seq and differential expression analyses. The high pith-thickness (PT) of the wheat stem could greatly enhance stem mechanical strength, especially the basal internodes which support the heavier upper part, such as upper stems, leaves and spikes. A QTL for PT in wheat was previously discovered on 3BL in a double haploid population of 'Westonia' × 'Kauz'. Here, a bulked segregant RNA-seq analysis was applied to identify candidate genes and develop associated SNP markers for PT. In this study, we aimed at screening differentially expressed genes (DEGs) and SNPs in the 3BL QTL interval. Sixteen DEGs were obtained based on BSR-seq and differential expression analyses. Twenty-four high-probability SNPs in eight genes were identified by comparing the allelic polymorphism in mRNA sequences between the high PT and low PT samples. Among them, six genes were confirmed to be associated with PT by qRT-PCR and sequencing. A putative vacuolar processing enzyme gene TaVPE3cB was screened out as a potential PT candidate gene in Australian wheat 'Westonia'. A robust SNP marker associated with TaVPE3cB was developed, which can assist in the introgression of TaVPE3cB.b in wheat breeding programs. In addition, we also discussed the function of other DEGs which may be related to pith development and programmed cell death (PCD). A five-level hierarchical regulation mechanism of stem pith PCD in wheat was proposed.
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Affiliation(s)
- Qier Liu
- Centre for Crop and Food Innovation, Food Futures Institute and College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, 6150, Australia
- Provincial Key Laboratory of Agrobiology, and Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People's Republic of China
| | - Yun Zhao
- Centre for Crop and Food Innovation, Food Futures Institute and College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, 6150, Australia
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, People's Republic of China
| | - Shanjida Rahman
- Centre for Crop and Food Innovation, Food Futures Institute and College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, 6150, Australia
| | - Maoyun She
- Centre for Crop and Food Innovation, Food Futures Institute and College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, 6150, Australia
| | - Jingjuan Zhang
- Centre for Crop and Food Innovation, Food Futures Institute and College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, 6150, Australia
| | - Rongchang Yang
- Centre for Crop and Food Innovation, Food Futures Institute and College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, 6150, Australia
| | - Shahidul Islam
- Centre for Crop and Food Innovation, Food Futures Institute and College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, 6150, Australia
| | - Graham O'Hara
- Centre for Crop and Food Innovation, Food Futures Institute and College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, 6150, Australia
| | - Rajeev K Varshney
- Centre for Crop and Food Innovation, Food Futures Institute and College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, 6150, Australia
| | - Hang Liu
- Centre for Crop and Food Innovation, Food Futures Institute and College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, 6150, Australia
| | - Hongxiang Ma
- Provincial Key Laboratory of Agrobiology, and Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People's Republic of China
| | - Wujun Ma
- Centre for Crop and Food Innovation, Food Futures Institute and College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, 6150, Australia.
- College of Agronomy, Qingdao Agriculture University, Qingdao, 266109, People's Republic of China.
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Ali S, Kucek LK, Riday H, Krom N, Krogman S, Cooper K, Jacobs L, Mehta P, Trammell M, Bhamidimarri S, Butler T, Saha MC, Monteros MJ. Transcript profiling of hairy vetch (Vicia villosa Roth) identified interesting genes for seed dormancy. THE PLANT GENOME 2023; 16:e20330. [PMID: 37125613 DOI: 10.1002/tpg2.20330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
Hairy vetch, a diploid annual legume species, has a robust growth habit, high biomass yield, and winter hardy characteristics. Seed hardness is a major constraint for growing hairy vetch commercially. Hard seeded cultivars are valuable as forages, whereas soft seeded and shatter resistant cultivars have advantages for their use as a cover crop. Transcript analysis of hairy vetch was performed to understand the genetic mechanisms associated with important hairy vetch traits. RNA was extracted from leaves, flowers, immature pods, seed coats, and cotyledons of contrasting soft and hard seeded "AU Merit" plants. A range of 31.22-79.18 Gb RNA sequence data per tissue sample were generated with estimated coverage of 1040-2639×. RNA sequence assembly and mapping of the contigs against the Medicago truncatula (V4.0) genome identified 76,422 gene transcripts. A total of 24,254 transcripts were constitutively expressed in hairy vetch tissues. Key genes, such as KNOX4 (a class II KNOTTED-like homeobox KNOXII gene), qHs1 (endo-1,4-β-glucanase), GmHs1-1 (calcineurin-like metallophosphoesterase), chitinase, shatterproof 1 and 2 (SHP1, SHP2), shatter resistant 1-5 (SHAT1-5)(NAC transcription factor), PDH1 (prephenate dehydrogenase 1), and pectin methylesterases with a potential role in seed hardness and pod shattering, were further explored based on genes involved in seed hardness from other species to query the hairy vetch transcriptome data. Identification of interesting candidate genes in hairy vetch can facilitate the development of improved cultivars with desirable seed characteristics for use as a forage and as a cover crop.
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Affiliation(s)
- Shahjahan Ali
- USDA-ARS, US Dairy Forage Research Center, Madison, Wisconsin, USA
| | | | | | - Nick Krom
- Noble Research Institute, LLC, Ardmore, Oklahoma, USA
| | - Sarah Krogman
- Noble Research Institute, LLC, Ardmore, Oklahoma, USA
| | | | - Lynne Jacobs
- Noble Research Institute, LLC, Ardmore, Oklahoma, USA
| | - Perdeep Mehta
- Noble Research Institute, LLC, Ardmore, Oklahoma, USA
| | - Michael Trammell
- Oklahoma State University Cooperative Extension, Shawnee, Oklahoma, USA
| | | | - Twain Butler
- Noble Research Institute, LLC, Ardmore, Oklahoma, USA
| | - Malay C Saha
- Noble Research Institute, LLC, Ardmore, Oklahoma, USA
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Raj SRG, Nadarajah K. QTL and Candidate Genes: Techniques and Advancement in Abiotic Stress Resistance Breeding of Major Cereals. Int J Mol Sci 2022; 24:ijms24010006. [PMID: 36613450 PMCID: PMC9820233 DOI: 10.3390/ijms24010006] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
At least 75% of the world's grain production comes from the three most important cereal crops: rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays). However, abiotic stressors such as heavy metal toxicity, salinity, low temperatures, and drought are all significant hazards to the growth and development of these grains. Quantitative trait locus (QTL) discovery and mapping have enhanced agricultural production and output by enabling plant breeders to better comprehend abiotic stress tolerance processes in cereals. Molecular markers and stable QTL are important for molecular breeding and candidate gene discovery, which may be utilized in transgenic or molecular introgression. Researchers can now study synteny between rice, maize, and wheat to gain a better understanding of the relationships between the QTL or genes that are important for a particular stress adaptation and phenotypic improvement in these cereals from analyzing reports on QTL and candidate genes. An overview of constitutive QTL, adaptive QTL, and significant stable multi-environment and multi-trait QTL is provided in this article as a solid framework for use and knowledge in genetic enhancement. Several QTL, such as DRO1 and Saltol, and other significant success cases are discussed in this review. We have highlighted techniques and advancements for abiotic stress tolerance breeding programs in cereals, the challenges encountered in introgressing beneficial QTL using traditional breeding techniques such as mutation breeding and marker-assisted selection (MAS), and the in roads made by new breeding methods such as genome-wide association studies (GWASs), the clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system, and meta-QTL (MQTL) analysis. A combination of these conventional and modern breeding approaches can be used to apply the QTL and candidate gene information in genetic improvement of cereals against abiotic stresses.
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Cheng W, Wang Z, Xu F, Lu G, Su Y, Wu Q, Wang T, Que Y, Xu L. Screening of Candidate Genes Associated with Brown Stripe Resistance in Sugarcane via BSR-seq Analysis. Int J Mol Sci 2022; 23:ijms232415500. [PMID: 36555141 PMCID: PMC9778799 DOI: 10.3390/ijms232415500] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/30/2022] [Accepted: 12/03/2022] [Indexed: 12/13/2022] Open
Abstract
Sugarcane brown stripe (SBS), caused by the fungal pathogen Helminthosporium stenospilum, is one of the most serious threats to sugarcane production. However, its outbreaks and epidemics require suitable climatic conditions, resulting in the inefficient improvement of the SBS resistance by phenotype selection. The sugarcane F1 population of SBS-resistant YT93-159 × SBS-susceptible ROC22 was used for constructing the bulks. Bulked segregant RNA-seq (BSR-seq) was then performed on the parents YT93-159 (T01) and ROC22 (T02), and the opposite bulks of 30 SBS-susceptible individuals mixed bulk (T03) and 30 SBS-resistant individuals mixed bulk (T04) collected from 287 F1 individuals. A total of 170.00 Gb of clean data containing 297,921 SNPs and 70,426 genes were obtained. Differentially expressed genes (DEGs) analysis suggested that 7787 and 5911 DEGs were identified in the parents (T01 vs. T02) and two mixed bulks (T03 vs. T04), respectively. In addition, 25,363 high-quality and credible SNPs were obtained using the genome analysis toolkit GATK for SNP calling. Subsequently, six candidate regions with a total length of 8.72 Mb, which were located in the chromosomes 4B and 7C of sugarcane wild species Saccharum spontaneum, were identified, and 279 genes associated with SBS-resistance were annotated by ED algorithm and ΔSNP-index. Furthermore, the expression profiles of candidate genes were verified by quantitative real-time PCR (qRT-PCR) analysis, and the results showed that eight genes (LRR-RLK, DHAR1, WRKY7, RLK1, BLH4, AK3, CRK34, and NDA2) and seven genes (WRKY31, CIPK2, CKA1, CDPK6, PFK4, CBL2, and PR2) of the 20 tested genes were significantly up-regulated in YT93-159 and ROC22, respectively. Finally, a potential molecular mechanism of sugarcane response to H. stenospilum infection is illustrate that the activations of ROS signaling, MAPK cascade signaling, Ca2+ signaling, ABA signaling, and the ASA-GSH cycle jointly promote the SBS resistance in sugarcane. This study provides abundant gene resources for the SBS resistance breeding in sugarcane.
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Affiliation(s)
| | | | | | | | | | | | | | - Youxiong Que
- Correspondence: (Y.Q.); (L.X.); Tel.: +86-591-8385-2547 (Y.Q.); +86-591-8377-2604 (L.X.)
| | - Liping Xu
- Correspondence: (Y.Q.); (L.X.); Tel.: +86-591-8385-2547 (Y.Q.); +86-591-8377-2604 (L.X.)
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Majeed A, Johar P, Raina A, Salgotra RK, Feng X, Bhat JA. Harnessing the potential of bulk segregant analysis sequencing and its related approaches in crop breeding. Front Genet 2022; 13:944501. [PMID: 36003337 PMCID: PMC9393495 DOI: 10.3389/fgene.2022.944501] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/28/2022] [Indexed: 12/26/2022] Open
Abstract
Most plant traits are governed by polygenes including both major and minor genes. Linkage mapping and positional cloning have contributed greatly to mapping genomic loci controlling important traits in crop species. However, they are low-throughput, time-consuming, and have low resolution due to which their efficiency in crop breeding is reduced. In this regard, the bulk segregant analysis sequencing (BSA-seq) and its related approaches, viz., quantitative trait locus (QTL)-seq, bulk segregant RNA-Seq (BSR)-seq, and MutMap, have emerged as efficient methods to identify the genomic loci/QTLs controlling specific traits at high resolution, accuracy, reduced time span, and in a high-throughput manner. These approaches combine BSA with next-generation sequencing (NGS) and enable the rapid identification of genetic loci for qualitative and quantitative assessments. Many previous studies have shown the successful identification of the genetic loci for different plant traits using BSA-seq and its related approaches, as discussed in the text with details. However, the efficiency and accuracy of the BSA-seq depend upon factors like sequencing depth and coverage, which enhance the sequencing cost. Recently, the rapid reduction in the cost of NGS together with the expected cost reduction of third-generation sequencing in the future has further increased the accuracy and commercial applicability of these approaches in crop improvement programs. This review article provides an overview of BSA-seq and its related approaches in crop breeding together with their merits and challenges in trait mapping.
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Affiliation(s)
- Aasim Majeed
- School of Agricultural Biotechnology, Punjab Agriculture University (PAU), Ludhiana, India
| | - Prerna Johar
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | - Aamir Raina
- Department of Botany, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - R. K. Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
- *Correspondence: R. K. Salgotra, ; Xianzhong Feng, ; Javaid Akhter Bhat,
| | - Xianzhong Feng
- Zhejiang Lab, Hangzhou, China
- *Correspondence: R. K. Salgotra, ; Xianzhong Feng, ; Javaid Akhter Bhat,
| | - Javaid Akhter Bhat
- Zhejiang Lab, Hangzhou, China
- International Genome Center, Jiangsu University, Zhenjiang, China
- *Correspondence: R. K. Salgotra, ; Xianzhong Feng, ; Javaid Akhter Bhat,
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Raineri J, Caraballo L, Rigalli N, Portapila M, Otegui ME, Chan RL. Expressing the sunflower transcription factor HaHB11 in maize improves waterlogging and defoliation tolerance. PLANT PHYSIOLOGY 2022; 189:230-247. [PMID: 35148415 PMCID: PMC9070847 DOI: 10.1093/plphys/kiac054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 01/17/2022] [Indexed: 06/01/2023]
Abstract
The sunflower (Helianthus annuus) transcription factor HaHB11 (H. annuus Homeobox 11) belongs to the homeodomain-leucine zipper family and confers improved yield to maize (Zea mays) hybrids (HiII × B73) and lines. Here we report that transgenic maize lines expressing HaHB11 exhibited better performance under waterlogging, both in greenhouse and field trials carried out during three growth cycles. Transgenic plants had increased chlorophyll content, wider stems, more nodal roots, greater total aerial biomass, a higher harvest index, and increased plant grain yield. Under severe defoliation caused by a windstorm during flowering, transgenic genotypes were able to set more grains than controls. This response was confirmed in controlled defoliation assays. Hybrids generated by crossing B73 HaHB11 lines with the contrasting Mo17 lines were also tested in the field and exhibited the same beneficial traits as the parental lines, compared with their respective controls. Moreover, they were less penalized by stress than commercial hybrids. Waterlogging tolerance increased via improvement of the root system, including more xylem vessels, reduced tissue damage, less superoxide accumulation, and altered carbohydrate metabolism. Multivariate analyses corroborated the robustness of the differential traits observed. Furthermore, canopy spectral reflectance data, computing 29 vegetation indices associated with biomass, chlorophyll, and abiotic stress, helped to distinguish genotypes as well as their growing conditions. Altogether the results reported here indicate that this sunflower gene constitutes a suitable tool to improve maize plants for environments prone to waterlogging and/or wind defoliation.
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Affiliation(s)
| | | | - Nicolás Rigalli
- CIFASIS, Universidad Nacional de Rosario—CONICET, Santa Fe 2000, Argentina
| | | | - María Elena Otegui
- Facultad de Agronomía, CONICET-INTA-FAUBA, Estación experimental Pergamino, Universidad de Buenos Aires, Buenos Aires C1417DSE, Argentina
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Cao A, de la Fuente M, Gesteiro N, Santiago R, Malvar RA, Butrón A. Genomics and Pathways Involved in Maize Resistance to Fusarium Ear Rot and Kernel Contamination With Fumonisins. FRONTIERS IN PLANT SCIENCE 2022; 13:866478. [PMID: 35586219 PMCID: PMC9108495 DOI: 10.3389/fpls.2022.866478] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/25/2022] [Indexed: 06/15/2023]
Abstract
Fusarium verticillioides is a causal agent of maize ear rot and produces fumonisins, which are mycotoxins that are toxic to animals and humans. In this study, quantitative trait loci (QTLs) and bulk-segregant RNA-seq approaches were used to uncover genomic regions and pathways involved in resistance to Fusarium ear rot (FER) and to fumonisin accumulation in maize kernels. Genomic regions at bins 4.07-4.1, 6-6.01, 6.04-6.05, and 8.05-8.08 were related to FER resistance and/or reduced fumonisin levels in kernels. A comparison of transcriptomes between resistant and susceptible inbred bulks 10 days after inoculation with F. verticillioides revealed 364 differentially expressed genes (DEGs). In the resistant inbred bulks, genes involved in sink metabolic processes such as fatty acid and starch biosynthesis were downregulated, as well as those involved in phytosulfokine signaling and many other genes involved in cell division; while genes involved in secondary metabolism and compounds/processes related to resistance were upregulated, especially those related to cell wall biosynthesis/rearrangement and flavonoid biosynthesis. These trends are indicative of a growth-defense trade-off. Among the DEGs, Zm00001d053603, Zm00001d035562, Zm00001d037810, Zm00001d037921, and Zm00001d010840 were polymorphic between resistant and susceptible bulks, were located in the confidence intervals of detected QTLs, and showed large differences in transcript levels between the resistant and susceptible bulks. Thus, they were identified as candidate genes involved in resistance to FER and/or reduced fumonisin accumulation.
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Affiliation(s)
- Ana Cao
- Misión Biológica de Galicia (CSIC), Pontevedra, Spain
| | | | | | - Rogelio Santiago
- Misión Biológica de Galicia (CSIC), Pontevedra, Spain
- Agrobiología Ambiental, Calidad de Suelos y Plantas (UVIGO), Unidad Asociada a la MBG (CSIC), Pontevedra, Spain
| | - Rosa Ana Malvar
- Misión Biológica de Galicia (CSIC), Pontevedra, Spain
- Agrobiología Ambiental, Calidad de Suelos y Plantas (UVIGO), Unidad Asociada a la MBG (CSIC), Pontevedra, Spain
| | - Ana Butrón
- Misión Biológica de Galicia (CSIC), Pontevedra, Spain
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Guan W, Shan J, Gao M, Guo J, Wu D, Zhang Q, Wang J, Chen R, Du B, Zhu L, He G. Bulked Segregant RNA Sequencing Revealed Difference Between Virulent and Avirulent Brown Planthoppers. FRONTIERS IN PLANT SCIENCE 2022; 13:843227. [PMID: 35498688 PMCID: PMC9047503 DOI: 10.3389/fpls.2022.843227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
The brown planthopper (Nilaparvata lugens Stål, BPH) is one of the most devastating insect pests of rice (Oryza sativa L.), but BPH populations have varying degrees of virulence to rice varieties carrying different resistance genes. To help efforts to characterize these variations we applied bulked segregant RNA sequencing (BSR-seq) to identify differentially expressed genes (DEGs) and genetic loci associated with BPH virulence to YHY15 rice plants carrying the resistance gene Bph15. BPHs that are highly virulent or avirulent to these plants were selected from an F2 population to form two contrasting bulks, and BSR-seq identified 751 DEGs between the bulks. Genes associated with carbohydrate, amino acid and nucleotide metabolism, the endocrine system, and signal transduction were upregulated in the avirulent insects when they fed on these plants. The results also indicated that shifts in lipid metabolism and digestive system pathways were crucial for the virulent BPHs' adaptation to the resistant rice. We identified 24 single-nucleotide polymorphisms (SNPs) in 21 genes linked with BPH virulence. Possible roles of genes apparently linked to BPH virulence are discussed. Our results provide potentially valuable information for further studies of BPH virulence mechanisms and development of robust control strategies.
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Chao H, Guo L, Zhao W, Li H, Li M. A major yellow-seed QTL on chromosome A09 significantly increases the oil content and reduces the fiber content of seed in Brassica napus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1293-1305. [PMID: 35084514 DOI: 10.1007/s00122-022-04031-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
A major yellow-seed QTL on chromosome A09 significantly increases the oil content and reduces the fiber content of seed in Brassica napus. The yellow-seed trait (YST) has always been a main breeding objective for rapeseed because yellow-seeded B. napus generally contains higher oil contents, fewer pigments and polyphenols and lower fiber content than black-seeded B. napus, although the mechanism controlling this correlation remains unclear. In this study, QTL mapping was implemented for YST based on a KN double haploid population derived from the hybridization of yellow-seeded B. napus N53-2 with a high oil content and black-seeded Ken-C8 with a relatively low oil content. Ten QTLs were identified, including four stable QTLs that could be detected in multiple environments. A major QTL, cqSC-A09, on chromosome A09 was identified by both QTL mapping and BSR-Seq technology, and explained more than 41% of the phenotypic variance. The major QTL cqSC-A09 for YST not only controls the seed color but also affects the oil and fiber contents in seeds. More importantly, the advantageous allele could increase the oil content and reduce the pigment and fiber content at the same time. This is the first QTL reported to control seed color, oil content and fiber content simultaneously with a large effect and has great application value for breeding high oil varieties with high seed quality. Important candidate genes, including BnaA09. JAZ1, BnaA09. GH3.3 and BnaA09. LOX3, were identified for cqSC-A09 by combining sequence variation annotation, expression differences and an interaction network, which lays a foundation for further cloning and breeding applications in the future.
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Affiliation(s)
- Hongbo Chao
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Liangxing Guo
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Weiguo Zhao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100, China
| | - Huaixin Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
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Xie X, Zhang X, Shen J, Du K. Poplar's Waterlogging Resistance Modeling and Evaluating: Exploring and Perfecting the Feasibility of Machine Learning Methods in Plant Science. FRONTIERS IN PLANT SCIENCE 2022; 13:821365. [PMID: 35222479 PMCID: PMC8874143 DOI: 10.3389/fpls.2022.821365] [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: 12/01/2021] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Floods, as one of the most common disasters in the natural environment, have caused huge losses to human life and property. Predicting the flood resistance of poplar can effectively help researchers select seedlings scientifically and resist floods precisely. Using machine learning algorithms, models of poplar's waterlogging tolerance were established and evaluated. First of all, the evaluation indexes of poplar's waterlogging tolerance were analyzed and determined. Then, significance testing, correlation analysis, and three feature selection algorithms (Hierarchical clustering, Lasso, and Stepwise regression) were used to screen photosynthesis, chlorophyll fluorescence, and environmental parameters. Based on this, four machine learning methods, BP neural network regression (BPR), extreme learning machine regression (ELMR), support vector regression (SVR), and random forest regression (RFR) were used to predict the flood resistance of poplar. The results show that random forest regression (RFR) and support vector regression (SVR) have high precision. On the test set, the coefficient of determination (R2) is 0.8351 and 0.6864, the root mean square error (RMSE) is 0.2016 and 0.2780, and the mean absolute error (MAE) is 0.1782 and 0.2031, respectively. Therefore, random forest regression (RFR) and support vector regression (SVR) can be given priority to predict poplar flood resistance.
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Affiliation(s)
- Xuelin Xie
- College of Sciences, Huazhong Agricultural University, Wuhan, China
| | | | - Jingfang Shen
- College of Sciences, Huazhong Agricultural University, Wuhan, China
| | - Kebing Du
- College of Horticulture and Forestry Sciences, Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, China
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Yang R, Li M, Harrison MT, Fahad S, Wei M, Li X, Yin L, Sha A, Zhou M, Liu K, Wang X. iTRAQ Proteomic Analysis of Wheat ( Triticum aestivum L.) Genotypes Differing in Waterlogging Tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:890083. [PMID: 35548301 PMCID: PMC9084233 DOI: 10.3389/fpls.2022.890083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 03/25/2022] [Indexed: 05/11/2023]
Abstract
Transient and chronic waterlogging constrains crop production in many regions of the world. Here, we invoke a novel iTRAQ-based proteomic strategy to elicit protein synthesis and regulation responses to waterlogging in tolerant (XM 55) and sensitive genotypes (YM 158). Of the 7,710 proteins identified, 16 were distinct between the two genotypes under waterlogging, partially defining a proteomic basis for waterlogging tolerance (and sensitivity). We found that 11 proteins were up-regulated and 5 proteins were down-regulated; the former included an Fe-S cluster assembly factor, heat shock cognate 70, GTP-binding protein SAR1A-like and CBS domain-containing protein. Down-regulated proteins contained photosystem II reaction center protein H, carotenoid 9, 10 (9', 10')-cleavage dioxygenase-like, psbP-like protein 1 and mitochondrial ATPase inhibitor. We showed that nine proteins responded to waterlogging with non-cultivar specificity: these included 3-isopropylmalate dehydratase large subunit, solanesyl-diphosphate synthase 2, DEAD-box ATP-dependent RNA helicase 3, and 3 predicted or uncharacterized proteins. Sixteen of the 28 selected proteins showed consistent expression patterns between mRNA and protein levels. We conclude that waterlogging stress may redirect protein synthesis, reduce chlorophyll synthesis and enzyme abundance involved in photorespiration, thus influencing synthesis of other metabolic enzymes. Collectively, these factors accelerate the accumulation of harmful metabolites in leaves in waterlogging-susceptible genotypes. The differentially expressed proteins enumerated here could be used as biological markers for enhancing waterlogging tolerance as part of future crop breeding programs.
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Affiliation(s)
- Rui Yang
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
- Agriculture College, Yangtze University, Jingzhou, China
| | - Murong Li
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
- Agriculture College, Yangtze University, Jingzhou, China
| | - Matthew Tom Harrison
- Tasmanian Institute of Agriculture, University of Tasmania, Burnie, TAS, Australia
| | - Shah Fahad
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
- Department of Agronomy, The University of Haripur, Haripur, Pakistan
- *Correspondence: Shah Fahad,
| | - Mingmei Wei
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
- Agriculture College, Yangtze University, Jingzhou, China
| | - Xiu Li
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
- Agriculture College, Yangtze University, Jingzhou, China
| | - Lijun Yin
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
- Agriculture College, Yangtze University, Jingzhou, China
| | - Aihua Sha
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Burnie, TAS, Australia
| | - Ke Liu
- Tasmanian Institute of Agriculture, University of Tasmania, Burnie, TAS, Australia
- Ke Liu,
| | - Xiaoyan Wang
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
- Agriculture College, Yangtze University, Jingzhou, China
- Xiaoyan Wang,
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Liu Y, Jiang T, Chen Y, Gu Y, Song F, Sun J, Luo J. Identification of Candidate Genes Associated With Hypoxia Tolerance in Trachinotus blochii Using Bulked Segregant Analysis and RNA-Seq. Front Genet 2022; 12:811685. [PMID: 34970306 PMCID: PMC8712738 DOI: 10.3389/fgene.2021.811685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 11/29/2021] [Indexed: 12/13/2022] Open
Abstract
Golden Pompano (Trachinotus blochii) has rapidly developed into the one of the main valuable fish species in Chinese marine aquaculture. Due to its rapid growth, active metabolism, and high oxygen consumption, hypoxia will increase its mortality and cause serious economic losses. We constructed two experimental groups of fish with different degrees of tolerance to hypoxia, used BSR-Seq analysis based on genome and genetic linkage groups to locate SNPs and genes that were related to the differences in hypoxia tolerance. The results showed that hypoxia tolerance SNPs of golden pompano may be jointly determined by multiple linkage groups, especially linkage groups 18 and 22. There were 768 and 348 candidate genes located in the candidate regions of the brain and liver, respectively. These genes were mainly involved in anaerobic energy metabolism, stress response, immune response, waste discharge, and cell death. The prostaglandin-endoperoxide synthase 2 (PTGS2) on LG8, which is involved in the metabolism of arachidonic acid, has a G/A nonsynonymous mutation at position 20641628, and the encoded amino acid was changed from hydrophobic aspartic acid to asparaginate. The specific pathway of the RIG-I-like receptor signaling pathway in the liver may mediate the metabolic system and the immune system, linking glucose metabolism with immune regulation. The death of the hypoxia-intolerant group may be due to the accumulation of lactic acid caused by the activation of anaerobic glycolysis during the early stage of hypoxia stress, and the activation of type I interferon was inhibited, which resulted in decreased immunity. Among the genes involved in the RIG-I-like receptor signaling pathway, the CYLD Lysine 63 Deubiquitinase (CYLD) located on LG16 had a G/T nonsynonymous mutation at position 13629651, and the encoded amino acid was changed from alanine acid to valine. The interferon induced with helicase C domain 1 (Ifih1) located on LG18 has a G/C nonsynonymous mutation at position 16153700, and the encoded hydrophilic glycine was changed to hydrophobic alanine. Our findings suggest these SNPs may assist in the molecular breeding of hypoxia-tolerant golden pompano, and speculate that the balance of glucose and lipid metabolism plays a key role in Trachinotus blochii under acute hypoxia.
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Affiliation(s)
- Yifan Liu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou, China
| | - Tian Jiang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou, China
| | - Youming Chen
- Hainan Blue Granary Technology Co., Ltd, Sanya, China
| | - Yue Gu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou, China
| | - Feibiao Song
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou, China
| | - Junlong Sun
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou, China
| | - Jian Luo
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou, China
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Tong C, Hill CB, Zhou G, Zhang XQ, Jia Y, Li C. Opportunities for Improving Waterlogging Tolerance in Cereal Crops-Physiological Traits and Genetic Mechanisms. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10081560. [PMID: 34451605 PMCID: PMC8401455 DOI: 10.3390/plants10081560] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/12/2021] [Accepted: 07/28/2021] [Indexed: 05/22/2023]
Abstract
Waterlogging occurs when soil is saturated with water, leading to anaerobic conditions in the root zone of plants. Climate change is increasing the frequency of waterlogging events, resulting in considerable crop losses. Plants respond to waterlogging stress by adventitious root growth, aerenchyma formation, energy metabolism, and phytohormone signalling. Genotypes differ in biomass reduction, photosynthesis rate, adventitious roots development, and aerenchyma formation in response to waterlogging. We reviewed the detrimental effects of waterlogging on physiological and genetic mechanisms in four major cereal crops (rice, maize, wheat, and barley). The review covers current knowledge on waterlogging tolerance mechanism, genes, and quantitative trait loci (QTL) associated with waterlogging tolerance-related traits, the conventional and modern breeding methods used in developing waterlogging tolerant germplasm. Lastly, we describe candidate genes controlling waterlogging tolerance identified in model plants Arabidopsis and rice to identify homologous genes in the less waterlogging-tolerant maize, wheat, and barley.
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Affiliation(s)
- Cen Tong
- Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia; (C.T.); (C.B.H.); (G.Z.); (X.-Q.Z.); (Y.J.)
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Camilla Beate Hill
- Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia; (C.T.); (C.B.H.); (G.Z.); (X.-Q.Z.); (Y.J.)
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Gaofeng Zhou
- Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia; (C.T.); (C.B.H.); (G.Z.); (X.-Q.Z.); (Y.J.)
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Xiao-Qi Zhang
- Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia; (C.T.); (C.B.H.); (G.Z.); (X.-Q.Z.); (Y.J.)
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Yong Jia
- Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia; (C.T.); (C.B.H.); (G.Z.); (X.-Q.Z.); (Y.J.)
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Chengdao Li
- Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia; (C.T.); (C.B.H.); (G.Z.); (X.-Q.Z.); (Y.J.)
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
- Department of Primary Industries and Regional Development, 3-Baron-Hay Court, South Perth, WA 6151, Australia
- Correspondence: ; Tel.: +61-893-607-519
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Guo Z, Zhou S, Wang S, Li WX, Du H, Xu Y. Identification of major QTL for waterlogging tolerance in maize using genome-wide association study and bulked sample analysis. J Appl Genet 2021; 62:405-418. [PMID: 33788096 DOI: 10.1007/s13353-021-00629-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 03/11/2021] [Accepted: 03/12/2021] [Indexed: 11/30/2022]
Abstract
Waterlogging has increasingly become one of the major constraints to maize (Zea mays L.) production in some maize growing areas as it seriously decreases the yield. Waterlogging tolerance in maize germplasm provides a basis for maize waterlogging improvement. In this study, nine seedling traits, plant height (PH), root length (RL), shoot dry weight (SDW), root dry weight (RDW), adventitious root number (ARN), node number of brace root (BRNN), brace root number (BRN), brace root dry weigh (BRDW), survival rate (SR), and the secondary traits that were defined as relative phenotypic value of seedling traits under waterlogging and control treatments were used in a natural population that contain 365 inbred lines to evaluate the waterlogging tolerance of tropical maize. The result showed that maize waterlogging tolerance was genetically controlled and seedling traits were significantly different between the control and waterlogging treatments. PH, RL, SDW, and RDW are important seedling traits for waterlogging tolerance identification. Some tropical maize inbred lines were identified with extreme waterlogging tolerance that can provide an important germplasm resource for breeding. Population structure analysis showed that two major phylogenetic subgroups in tropical maize could be identified. Genome-wide association study (GWAS) using 39,266 single nucleotide polymorphisms (SNPs) across the whole genome identified 49 trait-SNPs distributed on over all 10 chromosomes excluding chromosome 10. Seventy-one significant SNPs, distributed on all 10 chromosomes excluding chromosome 5, were identified by extend bulked sample analysis (Ext-BSA) based on the inbred lines with extreme phenotypes. GWAS and Ext-BSA identified the same loci on bin1.07, bin6.01, bin2.09, bin6.04, bin7.02, and bin7.03. Nine genes were proposed as potential candidate genes. Cloning and functional validation of these genes would be helpful for understanding the molecular mechanism of waterlogging tolerance in maize.
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Affiliation(s)
- Zifeng Guo
- Institute of Crop Science/CIMMYT-China, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.,National Maize Improvement Center, China Agricultural University, Beijing, 100094, China
| | - Shuangzhen Zhou
- Hubei collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
| | - Shanhong Wang
- Institute of Crop Science/CIMMYT-China, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wen-Xue Li
- Institute of Crop Science/CIMMYT-China, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hewei Du
- Hubei collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China.
| | - Yunbi Xu
- Institute of Crop Science/CIMMYT-China, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. .,International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, CP, 56130, México. .,CIMMYT-China Tropical Maize Research Center, Foshan University, Foshan, 528231, China.
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15
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Chen Y, Jia Y, Niu F, Wu Y, Ye J, Yang X, Zhang L, Song X. Identification and validation of genetic locus Rfk1 for wheat fertility restoration in the presence of Aegilops kotschyi cytoplasm. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:875-885. [PMID: 33392709 DOI: 10.1007/s00122-020-03738-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
Major fertility restorer locus for Aegilops kotschyi cytoplasm in wheat, Rfk1, was mapped to chromosome arm 1BS. Most likely candidate gene is TraesCS1B02G197400LC, which is predicted to encode a pectinesterase/pectinesterase inhibitor. Cytoplasmic male sterility (CMS) is widely used for heterosis and hybrid seed production in wheat. Genes related to male fertility restoration in the presence of Aegilops kotschyi cytoplasm have been reported, but the fertility restoration-associated gene loci have not been investigated systematically. In this study, a BC1F1 population derived from a backcross between KTP116A, its maintainer line TP116B, and its restorer line LK783 was employed to map fertility restoration by bulked segregant RNA-Seq (BSR-Seq). A major fertility allele restorer locus for Ae. kotschyi cytoplasm in wheat, Rfk1, was mapped to chromosome arm 1BS, and it was contributed by LK783. Morphological and cytological studies showed that male fertility restoration occurred mainly after the late uninucleate stage. Based on simple sequence repeat and single-nucleotide polymorphism genotyping, the gene locus was located between Xnwafu_6 and Xbarc137 on chromosome arm 1BS. To further isolate the specific region, six Kompetitive allele-specific polymerase chain reaction markers derived from BSR-Seq were developed to delimit Rfk1 within physical intervals of 26.0 Mb. After searching for differentially expressed genes within the candidate interval in the anthers and sequencing analysis, TraesCS1B02G197400LC was identified as a candidate gene for Rfk1 and it was predicted to encode a pectinesterase/pectinesterase inhibitor. Expression analysis also confirmed that it was specifically expressed in the anthers, and its expression level was higher in fertile lines compared with sterile lines. Thus, TraesCS1B02G197400LC was identified as the most likely candidate gene for Rfk1, thereby providing insights into the fertility restoration mechanism for K-type CMS in wheat.
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Affiliation(s)
- Yanru Chen
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Yulin Jia
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Fuqiang Niu
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Yongfeng Wu
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Jiali Ye
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Xuetong Yang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Lingli Zhang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.
| | - Xiyue Song
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.
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Lin M, Sun S, Fang J, Qi X, Sun L, Zhong Y, Sun Y, Hong G, Wang R, Li Y. BSR-Seq analysis provides insights into the cold stress response of Actinidia arguta F1 populations. BMC Genomics 2021; 22:72. [PMID: 33482717 PMCID: PMC7821520 DOI: 10.1186/s12864-021-07369-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 01/05/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Freezing injury, which is an important abiotic stress in horticultural crops, influences the growth and development and the production area of kiwifruit (Actinidia Lind1). Among Actinidia species, Actinidia arguta has excellent cold resistance, but knowledge relevant to molecular mechanisms is still limited. Understanding the mechanism underlying cold resistance in kiwifruit is important for breeding cold resistance. RESULTS In our study, a population resulting from the cross of A. arguta 'Ruby-3' × 'Kuilv' male was generated for kiwifruit hardiness study, and 20 cold-tolerant and 20 cold-sensitive populations were selected from 492 populations according to their LT50. Then, we performed bulked segregant RNA-seq combined with single-molecule real-time sequencing to identify differentially expressed genes that provide cold hardiness. We found that the content of soluble sucrose and the activity of β-amylase were higher in the cold-tolerant population than in the cold-sensitive population. Upon - 30 °C low-temperature treatment, 126 differentially expressed genes were identify; the expression of 59 genes was up-regulated and that of 67 genes was down-regulated between the tolerant and sensitive pools, respectively. KEGG pathway analysis showed that the DEGs were primarily related to starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism. Ten major key enzyme-encoding genes and two regulatory genes were up-regulated in the tolerant pool, and regulatory genes of the CBF pathway were found to be differentially expressed. In particular, a 14-3-3 gene was down-regulated and an EBF gene was up-regulated. To validate the BSR-Seq results, 24 DEGs were assessed via qRT-PCR, and the results were consistent with those obtained by BSR-Seq. CONCLUSION Our research provides valuable insights into the mechanism related to cold resistance in Actinidia and identified potential genes that are important for cold resistance in kiwifruit.
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Affiliation(s)
- Miaomiao Lin
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Shihang Sun
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Jinbao Fang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China.
| | - Xiujuan Qi
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China.
| | - Leiming Sun
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Yunpeng Zhong
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Yanxiang Sun
- Langfang Normal University, Langfang, 065000, China
| | - Gu Hong
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Ran Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Yukuo Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China
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Ko DK, Brandizzi F. A temporal hierarchy underpins the transcription factor-DNA interactome of the maize UPR. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:254-270. [PMID: 33098715 PMCID: PMC7942231 DOI: 10.1111/tpj.15044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 09/18/2020] [Accepted: 09/23/2020] [Indexed: 05/10/2023]
Abstract
Adverse environmental conditions reduce crop productivity and often increase the load of unfolded or misfolded proteins in the endoplasmic reticulum (ER). This potentially lethal condition, known as ER stress, is buffered by the unfolded protein response (UPR), a set of signaling pathways designed to either recover ER functionality or ignite programmed cell death. Despite the biological significance of the UPR to the life of the organism, the regulatory transcriptional landscape underpinning ER stress management is largely unmapped, especially in crops. To fill this significant knowledge gap, we performed a large-scale systems-level analysis of the protein-DNA interaction (PDI) network in maize (Zea mays). Using 23 promoter fragments of six UPR marker genes in a high-throughput enhanced yeast one-hybrid assay, we identified a highly interconnected network of 262 transcription factors (TFs) associated with significant biological traits and 831 PDIs underlying the UPR. We established a temporal hierarchy of TF binding to gene promoters within the same family as well as across different families of TFs. Cistrome analysis revealed the dynamic activities of a variety of cis-regulatory elements (CREs) in ER stress-responsive gene promoters. By integrating the cistrome results into a TF network analysis, we mapped a subnetwork of TFs associated with a CRE that may contribute to UPR management. Finally, we validated the role of a predicted network hub gene using the Arabidopsis system. The PDIs, TF networks, and CREs identified in our work are foundational resources for understanding transcription-regulatory mechanisms in the stress responses and crop improvement.
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Affiliation(s)
- Dae Kwan Ko
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, Michigan, 48824
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, 48824
| | - Federica Brandizzi
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, Michigan, 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, 48824
- Correspondence:
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18
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Wang JY, Chen JD, Wang SL, Chen L, Ma CL, Yao MZ. Repressed Gene Expression of Photosynthetic Antenna Proteins Associated with Yellow Leaf Variation as Revealed by Bulked Segregant RNA-seq in Tea Plant Camellia sinensis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:8068-8079. [PMID: 32633946 DOI: 10.1021/acs.jafc.0c01883] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The young leaves and shoots of albino tea cultivars are usually characterized as having a yellow or pale color, high amino acid, and low catechin. Increasing attention has been paid to albino tea cultivars in recent years because their tea generally shows high umami and reduced astringency. However, the genetic mechanism of yellow-leaf variation in albino tea cultivar has not been elucidated clearly. In this study, bulked segregant RNA-seq (BSR-seq) was performed on bulked yellow- and green-leaf hybrid progenies from a leaf color variation population. A total of 359 and 1134 differentially expressed genes (DEGs) were identified in the yellow and green hybrid bulked groups (Yf vs Gf) and parent plants (Yp vs Gp), respectively. The significantly smaller number of DEGs in Yf versus Gf than in Yp versus Gp indicated that individual differences could be reduced within the same hybrid progeny. Analysis of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes revealed that the photosynthetic antenna protein was most significantly enriched in either the bulked groups or their parents. Interaction was found among light-harvesting chlorophyll a/b -binding proteins (LHC), heat shock proteins (HSPs), and enzymes involved in cuticle formation. Combined with the transcriptomic expression profile, results showed that the repressed genes encoding LHC were closely linked to aberrant chloroplast development in yellow-leaf tea plants. Furthermore, the photoprotection and light stress response possessed by genes involved in HSP protein interaction and cuticle formation were discussed. The expression profile of DEGs was verified via quantitative real-time PCR analysis of the bulked samples and other F1 individuals. In summary, using BSR-seq on a hybrid population eliminated certain disturbing effects of genetic background and individual discrepancy, thereby helping this study to intensively focus on the key genes controlling leaf color variation in yellow-leaf tea plants.
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Affiliation(s)
- Jun-Ya Wang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Jie-Dan Chen
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Song-Lin Wang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Liang Chen
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Chun-Lei Ma
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Ming-Zhe Yao
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
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19
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Yi Q, Malvar RA, Álvarez-Iglesias L, Ordás B, Revilla P. Dissecting the genetics of cold tolerance in a multiparental maize population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:503-516. [PMID: 31740990 DOI: 10.1007/s00122-019-03482-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 11/11/2019] [Indexed: 05/21/2023]
Abstract
We identify the largest amount of QTLs for cold tolerance in maize; mainly associated with photosynthetic efficiency, which opens new possibilities for genomic selection for cold tolerance in maize. Breeding for cold tolerance in maize is an important objective in temperate areas. The objective was to carry out a highly efficient study of quantitative trait loci (QTLs) for cold tolerance in maize. We evaluated 406 recombinant inbred lines from a multi-parent advanced generation intercross (MAGIC) population in a growth chamber under cold and control conditions, and in the field at early and normal sowing. We recorded cold tolerance-related traits, including the number of days from sowing to emergence, chlorophyll content and maximum quantum efficiency of photosystem II (Fv/Fm). Association mapping was based on genotyping with near one million single nucleotide polymorphism (SNP) markers. We found 858 SNPs significantly associated with all traits, most of them under cold conditions and early sowing. Most QTLs were associated with chlorophyll and Fv/Fm. Many candidate genes coincided between the current research and previous reports. These results suggest that (1) the MAGIC population is an efficient tool for identifying QTLs for cold tolerance; (2) most QTLs for cold tolerance were associated with Fv/Fm; (3) most of these QTLs were located in specific genomic regions, particularly bin 10.04; (4) the current study allows genetically improving cold tolerance with genome-wide selection.
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Affiliation(s)
- Q Yi
- Misión Biológica de Galicia (CSIC), Apartado 28, 36080, Pontevedra, Spain
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - R A Malvar
- Misión Biológica de Galicia (CSIC), Apartado 28, 36080, Pontevedra, Spain
| | - L Álvarez-Iglesias
- Misión Biológica de Galicia (CSIC), Apartado 28, 36080, Pontevedra, Spain
| | - B Ordás
- Misión Biológica de Galicia (CSIC), Apartado 28, 36080, Pontevedra, Spain
| | - Pedro Revilla
- Misión Biológica de Galicia (CSIC), Apartado 28, 36080, Pontevedra, Spain.
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20
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Wei B, Bosland PW, Zhang Z, Wang Y, Zhang G, Wang L, Yu J. A predicted NEDD8 conjugating enzyme gene identified as a Capsicum candidate Rf gene using bulk segregant RNA sequencing. HORTICULTURE RESEARCH 2020; 7:210. [PMID: 35051251 PMCID: PMC7721708 DOI: 10.1038/s41438-020-00425-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 09/19/2020] [Accepted: 09/20/2020] [Indexed: 05/09/2023]
Abstract
Cytoplasmic male sterility (CMS) is an important tool for producing F1 hybrids, which can exhibit heterosis. The companion system, restorer-of-fertility (Rf), is poorly understood at the molecular level and would be valuable in producing restorer lines for hybrid seed production. The identity of the Rf gene in Capsicum (pepper) is currently unclear. In this study, using bulked segregant RNA sequencing (BSR-seq), a strong candidate Rf gene, Capana06g002866, which is annotated as a NEDD8 conjugating enzyme E2, was identified. Capana06g002866 has an ORF of 555 bp in length encoding 184 amino acids; it can be cloned from F1 plants from the hybridization of the CMS line 8A and restorer line R1 but is not found in CMS line 8A. With qRT-PCR validation, Capana06g002866 was found to be upregulated in restorer accessions compared to sterile accessions. The relative expression in flower buds increased with the developmental stage in F1 plants, while the expression was very low in all flower bud stages of the CMS lines. These results provide new insights into the Rf gene in pepper and will be useful for other crops utilizing the CMS system.
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Affiliation(s)
- Bingqiang Wei
- College of Horticulture, Gansu Agricultural University, 1 Yingmeng Village, Anning District, 730070 Lanzhou, China
| | - Paul W. Bosland
- Plant and Environmental Sciences Department, New Mexico State University, P.O. Box 30003, Las Cruces, 88001 NM USA
| | - Zhenghai Zhang
- Key Laboratory of Vegetable Genetics and Physiology of Ministry of the Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, 100081 Beijing, China
| | - Yongfu Wang
- College of Horticulture, Gansu Agricultural University, 1 Yingmeng Village, Anning District, 730070 Lanzhou, China
| | - Gaoyuan Zhang
- College of Horticulture, Gansu Agricultural University, 1 Yingmeng Village, Anning District, 730070 Lanzhou, China
| | - Lanlan Wang
- Vegetable Institute, Gansu Academy of Agricultural Sciences, 1 Nongkeyuan New Village, 730070 Lanzhou, China
| | - Jihua Yu
- College of Horticulture, Gansu Agricultural University, 1 Yingmeng Village, Anning District, 730070 Lanzhou, China
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21
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Wei B, Wang L, Bosland PW, Zhang G, Zhang R. Comparative transcriptional analysis of Capsicum flower buds between a sterile flower pool and a restorer flower pool provides insight into the regulation of fertility restoration. BMC Genomics 2019; 20:837. [PMID: 31711411 PMCID: PMC6849218 DOI: 10.1186/s12864-019-6210-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 10/22/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Cytoplasmic male sterility (CMS) and its restoration of fertility (Rf) system is an important mechanism to produce F1 hybrid seeds. Understanding the interaction that controls restoration at a molecular level will benefit plant breeders. The CMS is caused by the interaction between mitochondrial and nuclear genes, with the CMS phenotype failing to produce functional anthers, pollen, or male gametes. Thus, understanding the complex processes of anther and pollen development is a prerequisite for understanding the CMS system. Currently it is accepted that the Rf gene in the nucleus restores the fertility of CMS, however the Rf gene has not been cloned. In this study, CMS line 8A and the Rf line R1, as well as a sterile pool (SP) of accessions and a restorer pool (RP) of accessions analyzed the differentially expressed genes (DEGs) between CMS and its fertility restorer using the conjunction of RNA sequencing and bulk segregation analysis. RESULTS A total of 2274 genes were up-regulated in R1 as compared to 8A, and 1490 genes were up-regulated in RP as compared to SP. There were 891 genes up-regulated in both restorer accessions, R1 and RP, as compared to both sterile accessions, 8A and SP. Through annotation and expression analysis of co-up-regulated expressed genes, eight genes related to fertility restoration were selected. These genes encode putative fructokinase, phosphatidylinositol 4-phosphate 5-kinase, pectate lyase, exopolygalacturonase, pectinesterase, cellulose synthase, fasciclin-like arabinogalactan protein and phosphoinositide phospholipase C. In addition, a phosphatidylinositol signaling system and an inositol phosphate metabolism related to the fertility restorer of CMS were ranked as the most likely pathway for affecting the restoration of fertility in pepper. CONCLUSIONS Our study revealed that eight genes were related to the restoration of fertility, which provides new insight into understanding the molecular mechanism of fertility restoration of CMS in Capsicum.
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Affiliation(s)
- Bingqiang Wei
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Lanlan Wang
- Vegetable Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Paul W Bosland
- College of Agriculture, Consumer, and Environmental Sciences, New Mexico State University, Las Cruces, 88001, USA
| | - Gaoyuan Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, China
| | - Ru Zhang
- Vegetable Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
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22
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Gyawali A, Shrestha V, Guill KE, Flint-Garcia S, Beissinger TM. Single-plant GWAS coupled with bulk segregant analysis allows rapid identification and corroboration of plant-height candidate SNPs. BMC PLANT BIOLOGY 2019; 19:412. [PMID: 31590656 PMCID: PMC6781408 DOI: 10.1186/s12870-019-2000-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 08/30/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Genome wide association studies (GWAS) are a powerful tool for identifying quantitative trait loci (QTL) and causal single nucleotide polymorphisms (SNPs)/genes associated with various important traits in crop species. Typically, GWAS in crops are performed using a panel of inbred lines, where multiple replicates of the same inbred are measured and the average phenotype is taken as the response variable. Here we describe and evaluate single plant GWAS (sp-GWAS) for performing a GWAS on individual plants, which does not require an association panel of inbreds. Instead sp-GWAS relies on the phenotypes and genotypes from individual plants sampled from a randomly mating population. Importantly, we demonstrate how sp-GWAS can be efficiently combined with a bulk segregant analysis (BSA) experiment to rapidly corroborate evidence for significant SNPs. RESULTS In this study we used the Shoepeg maize landrace, collected as an open pollinating variety from a farm in Southern Missouri in the 1960's, to evaluate whether sp-GWAS coupled with BSA can efficiently and powerfully used to detect significant association of SNPs for plant height (PH). Plant were grown in 8 locations across two years and in total 768 individuals were genotyped and phenotyped for sp-GWAS. A total of 306 k polymorphic markers in 768 individuals evaluated via association analysis detected 25 significant SNPs (P ≤ 0.00001) for PH. The results from our single-plant GWAS were further validated by bulk segregant analysis (BSA) for PH. BSA sequencing was performed on the same population by selecting tall and short plants as separate bulks. This approach identified 37 genomic regions for plant height. Of the 25 significant SNPs from GWAS, the three most significant SNPs co-localize with regions identified by BSA. CONCLUSION Overall, this study demonstrates that sp-GWAS coupled with BSA can be a useful tool for detecting significant SNPs and identifying candidate genes. This result is particularly useful for species/populations where association panels are not readily available.
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Affiliation(s)
- Abiskar Gyawali
- Division of Biological Sciences, University of Missouri, Columbia, USA
| | - Vivek Shrestha
- Division of Biological Sciences, University of Missouri, Columbia, USA
| | | | - Sherry Flint-Garcia
- USDA-ARS, Columbia, MO USA
- Division of Plant Sciences, University of Missouri, Columbia, USA
| | - Timothy M. Beissinger
- Department of Crop Sciences, Georg-August Universität Göttingen, Göttingen, Germany
- Center for Integrated Breeding Research, Georg August Universität Göttingen, Göttingen, Germany
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A SNP Mutation of SiCRC Regulates Seed Number Per Capsule and Capsule Length of cs1 Mutant in Sesame. Int J Mol Sci 2019; 20:ijms20164056. [PMID: 31434218 PMCID: PMC6720709 DOI: 10.3390/ijms20164056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 08/12/2019] [Accepted: 08/15/2019] [Indexed: 11/16/2022] Open
Abstract
Seed number per capsule (SNC) is a major factor influencing seed yield and is an important trait with complex gene interaction effects. We first performed genetic analysis, gene cloning, and molecular mechanism study for an EMS-induced sesame mutant cs1 with fewer SNC and shorter capsule length (CL). The mutant traits were due to the pleiotropism of a regressive gene (Sics1). Capsule hormone determination showed that five out of 12 hormones, including auxin indole-3-acetic acid (IAA), had significantly different levels between wild type (WT) and mutant type (MT). KEGG pathway analysis showed that plant hormone signal transduction, especially the auxin signal transduction pathway, was the most abundant differentially expressed signaling pathway. After the cross-population association and regional genome screening, we found that three homozygous loci were retained in cs1. Further analysis of these three loci resulted in the identification of SiCRC as the candidate gene for cs1. SiCRC consists of seven exons and six introns encoding 163 amino acids. The SiCRC in cs1 showed a point mutation at intron 5 and exon 6 junction, resulting in the splice site being frame-shifted eight nucleotides further downstream, causing incorrect splicing. Taken together, we assumed the SNP mutation in SiCRC disrupted the function of the transcription factor, which might act downstream of the CRC-auxin signal transduction pathway, resulting in a shorter CL and less SNC mutation of cs1 in sesame. Our results highlight the molecular framework underlying the transcription factor CRC-mediated role of auxin transduction in SNC and CL development.
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24
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Fukao T, Barrera-Figueroa BE, Juntawong P, Peña-Castro JM. Submergence and Waterlogging Stress in Plants: A Review Highlighting Research Opportunities and Understudied Aspects. FRONTIERS IN PLANT SCIENCE 2019; 10:340. [PMID: 30967888 PMCID: PMC6439527 DOI: 10.3389/fpls.2019.00340] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 03/05/2019] [Indexed: 05/20/2023]
Abstract
Soil flooding creates composite and complex stress in plants known as either submergence or waterlogging stress depending on the depth of the water table. In nature, these stresses are important factors dictating the species composition of the ecosystem. On agricultural land, they cause economic damage associated with long-term social consequences. The understanding of the plant molecular responses to these two stresses has benefited from research studying individual components of the stress, in particular low-oxygen stress. To a lesser extent, other associated stresses and plant responses have been incorporated into the molecular framework, such as ion and ROS signaling, pathogen susceptibility, and organ-specific expression and development. In this review, we aim to highlight known or suspected components of submergence/waterlogging stress that have not yet been thoroughly studied at the molecular level in this context, such as miRNA and retrotransposon expression, the influence of light/dark cycles, protein isoforms, root architecture, sugar sensing and signaling, post-stress molecular events, heavy-metal and salinity stress, and mRNA dynamics (splicing, sequestering, and ribosome loading). Finally, we explore biotechnological strategies that have applied this molecular knowledge to develop cultivars resistant to flooding or to offer alternative uses of flooding-prone soils, like bioethanol and biomass production.
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Affiliation(s)
- Takeshi Fukao
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | | | - Piyada Juntawong
- Center for Advanced Studies in Tropical Natural Resources, National Research University – Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Julián Mario Peña-Castro
- Laboratorio de Biotecnología Vegetal, Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec, Mexico
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25
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Tan C, Liu Z, Huang S, Feng H. Mapping of the male sterile mutant gene ftms in Brassica rapa L. ssp. pekinensis via BSR-Seq combined with whole-genome resequencing. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:355-370. [PMID: 30382313 DOI: 10.1007/s00122-018-3223-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 10/25/2018] [Indexed: 05/19/2023]
Abstract
A male sterile mutant was created by 60Co γ-rays of microspores isolated from Chinese cabbage DH line 'FT'. A candidate gene for the male sterile trait was identified as Bra010198. Male sterility is used for hybrid seed production in Chinese cabbage. In this study, we derived a male sterile mutant (ftms) from Chinese cabbage DH line 'FT' by irradiating microspores with 60Co γ-rays and realized the rapid trait transformation from male fertility to sterility for creating valuable breeding materials. Genetic analysis indicated that the male sterile trait is controlled by a single recessive nuclear gene, ftms. Microspore development in mutant ftms was aborted at the tetrad stage and associated with severely retarded degeneration and vacuolation of tapetum. Using BSR-seq analysis, the candidate region for ftms was mapped on chromosome A05. A large F2 population was created, and the region was narrowed to approximately 1.7-Mb between markers Indel20 and Indel14 via linkage analysis. The recombination frequency was extremely suppressed because the region was located on the chromosome A05 centromere. Whole-genome resequencing of mutant ftms and wild-type 'FT' aligned only one nonsynonymous SNP to Bra010198; this gene is a homolog of Arabidopsis KNS4/UPEX1, which encodes a putative β-(1,3)-galactosyltransferase that controls pollen exine development. Comparative sequencing verified the SNP position on the fifth exon of Bra010198 in mutant ftms. Further genotyping revealed that the male sterile phenotype was fully co-segregated with this SNP. Quantitative real-time PCR indicated that Bra0101918 specifically expressed in stamen. The data presented herein suggested that Bra010198 is a strong candidate gene for ftms. Hence, we developed a male sterile line for potential application in breeding and expanded the knowledge about the molecular mechanism underlying male sterility in Chinese cabbage.
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Affiliation(s)
- Chong Tan
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Zhiyong Liu
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Shengnan Huang
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Hui Feng
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China.
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26
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Dakouri A, Zhang X, Peng G, Falk KC, Gossen BD, Strelkov SE, Yu F. Analysis of genome-wide variants through bulked segregant RNA sequencing reveals a major gene for resistance to Plasmodiophora brassicae in Brassica oleracea. Sci Rep 2018; 8:17657. [PMID: 30518770 PMCID: PMC6281628 DOI: 10.1038/s41598-018-36187-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 11/10/2018] [Indexed: 12/22/2022] Open
Abstract
Two cabbage (Brassica oleracea) cultivars 'Tekila' and 'Kilaherb' were identified as resistant to several pathotypes of Plasmodiophora brassicae. In this study, we identified a clubroot resistance gene (Rcr7) in 'Tekila' for resistance to pathotype 3 of P. brassicae from a segregating population derived from 'Tekila' crossed with the susceptible line T010000DH3. Genetic mapping was performed by identifying the percentage of polymorphic variants (PPV), a new method proposed in this study, through bulked segregant RNA sequencing. Chromosome C7 carried the highest PPV (42%) compared to the 30-34% in the remaining chromosomes. A peak with PPV (56-73%) was found within the physical interval 41-44 Mb, which indicated that Rcr7 might be located in this region. Kompetitive Allele-Specific PCR was used to confirm the association of Rcr7 with SNPs in the region. Rcr7 was flanked by two SNP markers and co-segregated with three SNP markers in the segregating population of 465 plants. Seven genes encoding TIR-NBS-LRR disease resistance proteins were identified in the target region, but only two genes, Bo7g108760 and Bo7g109000, were expressed. Resistance to pathotype 5X was also mapped to the same region as Rcr7. B. oleracea lines including 'Kilaherb' were tested with five SNP markers for Rcr7 and for resistance to pathotype 3; 11 of 25 lines were resistant, but 'Kilaherb' was the only line that carried the SNP alleles associated with Rcr7. The presence of Rcr7 in 'Kilaherb' for resistance to both pathotypes 3 and 5X was confirmed through linkage analysis.
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Affiliation(s)
- Abdulsalam Dakouri
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Canada
| | - Xingguo Zhang
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Canada
- The college of Agronomy, Henan Agricultural University, Nanyang, China
| | - Gary Peng
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Canada
| | - Kevin C Falk
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Canada
| | - Bruce D Gossen
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Canada
| | - Stephen E Strelkov
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Alberta, Canada
| | - Fengqun Yu
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Canada.
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27
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Nishijima R, Yoshida K, Sakaguchi K, Yoshimura SI, Sato K, Takumi S. RNA Sequencing-Based Bulked Segregant Analysis Facilitates Efficient D-genome Marker Development for a Specific Chromosomal Region of Synthetic Hexaploid Wheat. Int J Mol Sci 2018; 19:E3749. [PMID: 30486239 PMCID: PMC6321645 DOI: 10.3390/ijms19123749] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 11/20/2018] [Accepted: 11/22/2018] [Indexed: 11/16/2022] Open
Abstract
Common wheat originated from interspecific hybridization between cultivated tetraploid wheat and its wild diploid relative Aegilops tauschii followed by amphidiploidization. This evolutionary process can be reproduced artificially, resulting in synthetic hexaploid wheat lines. Here we performed RNA sequencing (RNA-seq)-based bulked segregant analysis (BSA) using a bi-parental mapping population of two synthetic hexaploid wheat lines that shared identical A and B genomes but included with D-genomes of distinct origins. This analysis permitted identification of D-genome-specific polymorphisms around the Net2 gene, a causative locus to hybrid necrosis. The resulting single nucleotide polymorphisms (SNPs) were classified into homoeologous polymorphisms and D-genome allelic variations, based on the RNA-seq results of a parental tetraploid and two Ae. tauschii accessions. The difference in allele frequency at the D-genome-specific SNP sites between the contrasting bulks (ΔSNP-index) was higher on the target chromosome than on the other chromosomes. Several SNPs with the highest ΔSNP-indices were converted into molecular markers and assigned to the Net2 chromosomal region. These results indicated that RNA-seq-based BSA can be applied efficiently to a synthetic hexaploid wheat population to permit molecular marker development in a specific chromosomal region of the D genome.
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Affiliation(s)
- Ryo Nishijima
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe 657-8501, Japan.
| | - Kentaro Yoshida
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe 657-8501, Japan.
| | - Kohei Sakaguchi
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe 657-8501, Japan.
| | - Shin-Ichi Yoshimura
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe 657-8501, Japan.
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan.
| | - Shigeo Takumi
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe 657-8501, Japan.
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28
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Abstract
A major problem of climate change is the increasing duration and frequency of heavy rainfall events. This leads to soil flooding that negatively affects plant growth, eventually leading to death of plants if the flooding persists for several days. Most crop plants are very sensitive to flooding, and dramatic yield losses occur due to flooding each year. This review summarizes recent progress and approaches to enhance crop resistance to flooding. Most experiments have been done on maize, barley, and soybean. Work on other crops such as wheat and rape has only started. The most promising traits that might enhance crop flooding tolerance are anatomical adaptations such as aerenchyma formation, the formation of a barrier against radial oxygen loss, and the growth of adventitious roots. Metabolic adaptations might be able to improve waterlogging tolerance as well, but more studies are needed in this direction. Reasonable approaches for future studies are quantitative trait locus (QTL) analyses or genome-wide association (GWA) studies in combination with specific tolerance traits that can be easily assessed. The usage of flooding-tolerant relatives or ancestral cultivars of the crop of interest in these experiments might enhance the chances of finding useful tolerance traits to be used in breeding.
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