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Zhang Z, An D, Yu H, Sun L, Cao Y, Zhang B, Wang L. Fine mapping of Rf2, a minor Restorer-of-fertility (Rf) gene for cytoplasmic male sterility in chili pepper G164 (Capsicum annuum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2699-2709. [PMID: 35710637 DOI: 10.1007/s00122-022-04143-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 05/28/2022] [Indexed: 06/15/2023]
Abstract
Genome re-sequencing and recombination analyses identified Capana06g000193 as a strong candidate for the minor male fertility restoration locus Rf2 in chili pepper G164 harboring two dominant male fertility restoration genes. Male fertility restoration genes of chili pepper restorer line G164 (Capsicum annuum L.) were studied using molecular marker genotypes of an F2 population (7G) of G164 crossed with the cytoplasmic male sterility line 77013A. The ratio of sterile to fertile single plants in the F2 population was 1:15. This result indicates that chili pepper G164 has two dominant restoration genes, which we designated as Rf1 and Rf2. An individual plant recessive for Rf1 and heterozygous for Rf2, 7G-112 (rf1rf1Rf2rf2), was identified by molecular marker selection and genetic analysis, and a single Rf2 gene-segregating population with a 3:1 ratio of fertile to sterile plants was developed from the self-pollination of male fertile individuals of 77013A and 7G-112 hybrid progeny. Bulk segregant analysis of fertile and sterile pools from the segregating populations was used to genetically map Rf2 to a 3.1-Mb region on chromosome 6. Rf2 was further narrowed to a 179.3-kb interval through recombination analysis of molecular markers and obtained the most likely candidate gene, Capana06g000193.
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Affiliation(s)
- Zhenghai Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081, China
| | - Dongliang An
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081, China
| | - Hailong Yu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081, China
| | - Liuqing Sun
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081, China
| | - Yacong Cao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081, China
| | - Baoxi Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081, China
| | - Lihao Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081, China.
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Zhang Z, An D, Cao Y, Yu H, Zhu Y, Mei Y, Zhang B, Wang L. Development and application of KASP markers associated with Restorer-of-fertility gene in Capsicum annuum L. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2757-2765. [PMID: 35035134 PMCID: PMC8720122 DOI: 10.1007/s12298-021-01109-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/08/2021] [Accepted: 11/25/2021] [Indexed: 05/09/2023]
Abstract
Fertility restoration of cytoplasmic male sterility (CMS) in Capsicum annuum is controlled by multiple alleles of Restorer-of-fertility (Rf) genes. The isolation of additional Rf genes should therefore enrich the knowledge of CMS/Rf systems and accelerate their exploitation in hybrid seed production. In this study, the fertility restorer gene CaRfm of '0601 M', a non-pungent bell pepper, was genetically mapped to a 1.2-cM region flanked by KASP markers S761 and S183. CaRfm was then physically mapped to a 128.96-Kb interval predicted from 24 recombinants with two co-segregated markers, S423 and S424. CaPPR6 encoding a pentatricopeptide repeat (PPR) protein was suggested as the most likely candidate gene for the CaRfm locus on the basis of sequence alignment as well as genotyping of tightly linked markers. In addition, molecular markers S1597 and S1609, which are immediately adjacent to CaRfm at 15.7 and 57.8-Kb respectively, were developed and applied to marker-assisted selection. The results provided friendly markers for breeding pepper restorer lines and laid the foundation for elucidating the male fertility restoration mechanism. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01109-9.
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Affiliation(s)
- Zhenghai Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081 China
| | - Dongliang An
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081 China
| | - Yacong Cao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081 China
| | - Hailong Yu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081 China
| | - Yanshu Zhu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081 China
| | - Yajie Mei
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081 China
| | - Baoxi Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081 China
| | - Lihao Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081 China
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Vendelbo NM, Mahmood K, Sarup P, Kristensen PS, Orabi J, Jahoor A. Genomic Scan of Male Fertility Restoration Genes in a 'Gülzow' Type Hybrid Breeding System of Rye ( Secale cereale L.). Int J Mol Sci 2021; 22:ijms22179277. [PMID: 34502186 PMCID: PMC8431178 DOI: 10.3390/ijms22179277] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 02/03/2023] Open
Abstract
Efficient and stable restoration of male fertility (Rf) is a prerequisite for large-scale hybrid seed production but remains an inherent issue in the predominant fertility control system of rye (Secale cereale L.). The ‘Gülzow’ (G)-type cytoplasmic male sterility (CMS) system in hybrid rye breeding exhibits a superior Rf. While having received little scientific attention, one major G-type Rf gene has been identified on 4RL (Rfg1) and two minor genes on 3R (Rfg2) and 6R (Rfg3) chromosomes. Here, we report a comprehensive investigation of the genetics underlying restoration of male fertility in a large G-type CMS breeding system using recent advents in rye genomic resources. This includes: (I) genome-wide association studies (GWAS) on G-type germplasm; (II) GWAS on a biparental mapping population; and (III) an RNA sequence study to investigate the expression of genes residing in Rf-associated regions in G-type rye hybrids. Our findings provide compelling evidence of a novel major G-type non-PPR Rf gene on the 3RL chromosome belonging to the mitochondrial transcription termination factor gene family. We provisionally denote the identified novel Rf gene on 3RL RfNOS1. The discovery made in this study is distinct from known P- and C-type systems in rye as well as recognized CMS systems in barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.). We believe this study constitutes a stepping stone towards understanding the restoration of male fertility in the G-type CMS system and potential resources for addressing the inherent issues of the P-type system.
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Affiliation(s)
- Nikolaj Meisner Vendelbo
- Nordic Seed A/S, Grindsnabevej 25, 8300 Odder, Denmark; (K.M.); (P.S.); (P.S.K.); (J.O.); (A.J.)
- Department of Agroecology, Faculty of Technology, Aarhus University, Forsøgsvej 1, Flakkebjerg, 4200 Slagelse, Denmark
- Correspondence:
| | - Khalid Mahmood
- Nordic Seed A/S, Grindsnabevej 25, 8300 Odder, Denmark; (K.M.); (P.S.); (P.S.K.); (J.O.); (A.J.)
| | - Pernille Sarup
- Nordic Seed A/S, Grindsnabevej 25, 8300 Odder, Denmark; (K.M.); (P.S.); (P.S.K.); (J.O.); (A.J.)
| | - Peter Skov Kristensen
- Nordic Seed A/S, Grindsnabevej 25, 8300 Odder, Denmark; (K.M.); (P.S.); (P.S.K.); (J.O.); (A.J.)
| | - Jihad Orabi
- Nordic Seed A/S, Grindsnabevej 25, 8300 Odder, Denmark; (K.M.); (P.S.); (P.S.K.); (J.O.); (A.J.)
| | - Ahmed Jahoor
- Nordic Seed A/S, Grindsnabevej 25, 8300 Odder, Denmark; (K.M.); (P.S.); (P.S.K.); (J.O.); (A.J.)
- Department of Plant Breeding, The Swedish University of Agricultural Sciences, 23053 Alnarp, Sweden
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Niedziela A, Brukwiński W, Bednarek PT. Genetic mapping of pollen fertility restoration QTLs in rye (Secale cereale L.) with CMS Pampa. J Appl Genet 2021; 62:185-198. [PMID: 33409933 PMCID: PMC8032618 DOI: 10.1007/s13353-020-00599-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/16/2020] [Accepted: 11/23/2020] [Indexed: 11/24/2022]
Abstract
Cytoplasmic male sterility (CMS) is a widely applied plant breeding tool for hybrid seed production. The phenomenon is often caused by chimeric genes with altered open reading frames (ORFs) located in the mitochondrial genomes and expressed as novel genotoxic products that induce pollen abortion. The fertility of CMS plants can be restored by nuclear-encoded genes that inhibit the action of ORFs responsible for pollen sterility. A recombinant inbred line (RIL) mapping population S64/04/01, encompassing 175 individuals, was used for genetic map construction and identification of quantitative trait loci (QTLs) responsible for fertility restoration in rye (Secale cereale L.) with CMS Pampa. The genetic map of all seven rye chromosomes included 15,516 SNP and silicoDArT markers and covered 1070.5 cm. Individual QTLs explaining 60% and 5.5% of the fertility trait’s phenotypic variance were mapped to chromosomes 4R (QRft-4R) and 5R (QRft-5R), respectively. Association mapping identified markers with the highest R2 value of 0.58 (p value = 2.21E-28). Markers showing the highest associations with the trait were also mapped to the 4R chromosome within the QRft-4R region. Based on marker sequence homology, putative genes involved in pollen fertility restoration were suggested. Five silicoDArTs were converted into PCR-based markers for further breeding purposes.
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Affiliation(s)
- Agnieszka Niedziela
- Plant Breeding and Acclimatization Institute, NRI, Radzików, 05-870, Błonie, Poland
| | | | - Piotr Tomasz Bednarek
- Plant Breeding and Acclimatization Institute, NRI, Radzików, 05-870, Błonie, Poland.
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5
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Zhang Z, Zhu Y, Cao Y, Yu H, Bai R, Zhao H, Zhang B, Wang L. Fine mapping of the male fertility restoration gene CaRf032 in Capsicum annuum L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1177-1187. [PMID: 31925462 DOI: 10.1007/s00122-020-03540-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 01/07/2020] [Indexed: 05/24/2023]
Abstract
A novel strong candidate gene CA00g82510 for the male fertility restoration locus CaRf032 in Capsicum annuum was identified by genome re-sequencing and recombination analysis. A single dominant locus (CaRf032) for fertility restoration of cytoplasmic male sterility was identified in the strong restorer inbred line IVF2014032 of chili pepper (Capsicum annuum L.). CaRf032 was localized within an 8.81-Mb candidate intervals on chromosome 6 using bulked segregant analysis based on high-throughput sequencing data. Subsequently, the candidate interval was genetically mapped and defined to a 249.41-kb region using an F2 population of 441 individuals generated by crossing the male-sterile line 77013A and the restorer line IVF2014032. To fine map CaRf032, eight newly developed KASP markers were used to genotype 23 recombinants screened from a larger F2 population of 2877 individuals. The CaRf032 locus was localized to a 148.05-kb region between the KASP markers S1402 and S1354, which was predicted to contain 22 open reading frames (ORFs). One ORF with an incomplete sequence was predicted to contain a PPR motif, and its physical position overlapped with the Rf candidate gene CaPPR6_46. The PPR ORF sequence before the gap showed 100% identity with the CA00g82510 locus of the CM334 reference genome. CA00g82510 encodes a protein of 583 amino acids, containing 14 PPR motifs, and shows significantly differential expression between the flower buds of the maintainer line 77013 and the restorer line IVF2014032. These results indicated that CA00g82510 is a strong candidate gene for CaRf032. Five KASP markers, which detected single-nucleotide polymorphisms in CA00g82510 of 77013 and IVF2014032, co-segregated with CaRf032 and showed 64.4% successful genotyping of 38 maintainer and 63 restorer lines.
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Affiliation(s)
- 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, Beijing, 100081, China
| | - Yanshu Zhu
- 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, Beijing, 100081, China
| | - Yacong Cao
- 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, Beijing, 100081, China
| | - Hailong Yu
- 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, Beijing, 100081, China
| | - Ruiqin Bai
- 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, Beijing, 100081, China
| | - Hong Zhao
- 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, Beijing, 100081, China
| | - Baoxi 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, Beijing, 100081, China
| | - Lihao Wang
- 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, Beijing, 100081, China.
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6
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Rodríguez-Suárez C, Bagnaresi P, Cattivelli L, Pistón F, Castillo A, Martín AC, Atienza SG, Ramírez C, Martín A. Transcriptomics, chromosome engineering and mapping identify a restorer-of-fertility region in the CMS wheat system msH1. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:283-295. [PMID: 31624874 DOI: 10.1007/s00122-019-03457-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 10/09/2019] [Indexed: 05/24/2023]
Abstract
An original RNA-seq mapping strategy, validated with chromosome engineering and physical mapping, identifies candidate genes for fertility restoration in the 6HchS chromosome of Hordeum chilense in the wheat msH1 system. Cytoplasmic male sterility (CMS) is a valuable trait for hybrid seed production. The msH1 CMS system in common wheat results from the incompatibility between the nuclear genome of wheat and the cytoplasm of the wild barley Hordeum chilense. This work aims to identify H. chilense candidate genes for fertility restoration in the msH1 system with a multidisciplinary strategy based on chromosome engineering, differential expression analysis and genome mapping. Alloplasmic isogenic wheat lines differing for fertility, associated with the presence of an acrocentric chromosome Hchac resulting from the rearrangement of the short arms of H. chilense chromosomes 1Hch and 6Hch, were used for transcriptome sequencing. Two novel RNA-seq mapping approaches were designed and compared to identify differentially expressed genes of H. chilense associated with male fertility restoration. Minichromosomes (Hchmi), new smaller reorganizations of the Hchac also restoring fertility, were obtained and used to validate the candidate genes. This strategy was successful identifying a putative restorer-of-fertility region on 6HchS, with six candidate genes, including the ortholog of the barley restorer gene Rfm1. Additionally, transcriptomics gave preliminary insights on sterility and restoration networks showing the importance of energy supply, stress, protein metabolism and RNA processing.
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Affiliation(s)
- Cristina Rodríguez-Suárez
- Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (IAS-CSIC), Avda. Menéndez Pidal s/n, 14080, Córdoba, Spain.
| | - Paolo Bagnaresi
- Research Centre for Genomics and Bioinformatics, Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Via S. Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - Luigi Cattivelli
- Research Centre for Genomics and Bioinformatics, Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Via S. Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - Fernando Pistón
- Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (IAS-CSIC), Avda. Menéndez Pidal s/n, 14080, Córdoba, Spain
| | - Almudena Castillo
- Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (IAS-CSIC), Avda. Menéndez Pidal s/n, 14080, Córdoba, Spain
| | - Azahara C Martín
- Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Sergio G Atienza
- Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (IAS-CSIC), Avda. Menéndez Pidal s/n, 14080, Córdoba, Spain
| | - Carmen Ramírez
- Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (IAS-CSIC), Avda. Menéndez Pidal s/n, 14080, Córdoba, Spain
| | - Antonio Martín
- Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (IAS-CSIC), Avda. Menéndez Pidal s/n, 14080, Córdoba, Spain
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7
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Bernhard T, Koch M, Snowdon RJ, Friedt W, Wittkop B. Undesired fertility restoration in msm1 barley associates with two mTERF genes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1335-1350. [PMID: 30659305 DOI: 10.1007/s00122-019-03281-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/07/2019] [Indexed: 05/02/2023]
Abstract
The novel Rfm3 locus causing undesired fertility restoration in the msm1 cytoplasm of winter barley is located on the short arm of chromosome 6H. Undesired fertility restoration of cytoplasmic male sterile (CMS) mother lines in absence of the functional Rfm1 restorer gene is a significant problem for hybrid breeding in winter barley. Here, we describe that a novel restorer locus on the short arm of chromosome 6H, designated Rfm3, is closely linked to two mitochondrial transcription termination factor family (mTERF) protein coding genes. Genome-wide association studies in a multiparental mapping population revealed that two of the most significantly associated markers are located very close to these genes, with one marker lying directly within one mTERF gene sequence. Sequences of the candidate genes in the parental lines, segregating individuals and an independent set of breeding lines clearly revealed haplotypes discriminating completely sterile, partially fertile and Rfm1-restorer lines. The haplotypes segregate for several single nucleotide polymorphisms, a 6 bp insertion-deletion (InDel) polymorphism and another 2 bp InDel. CMS-unstable genotypes carrying haplotypes associated with undesired fertility restoration showed significantly higher grain setting on bagged spikes when plants were subjected to elevated temperatures during anthesis, indicating a temperature influence on pollen fertility. SNPs associated with desirable Rfm3 haplotypes can be implemented in marker-assisted selection of stable CMS mother lines.
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Affiliation(s)
- Timm Bernhard
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
| | - Michael Koch
- Deutsche Saatveredelung AG, Thueler Str. 30, 33154, Salzkotten, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Wolfgang Friedt
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Benjamin Wittkop
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
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8
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Melonek J, Zhou R, Bayer PE, Edwards D, Stein N, Small I. High intraspecific diversity of Restorer-of-fertility-like genes in barley. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:281-295. [PMID: 30276910 PMCID: PMC7380019 DOI: 10.1111/tpj.14115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/25/2018] [Accepted: 09/26/2018] [Indexed: 05/24/2023]
Abstract
Nuclear restorer of fertility (Rf) genes suppress the effects of mitochondrial genes causing cytoplasmic male sterility (CMS), a condition in which plants fail to produce viable pollen. Rf genes, many of which encode RNA-binding pentatricopeptide repeat (PPR) proteins, are applied in hybrid breeding to overcome CMS used to block self-pollination of the seed parent. Here, we characterise the repertoire of restorer-of-fertility-like (RFL) PPR genes in barley (Hordeum vulgare). We found 26 RFL genes in the reference genome ('Morex') and an additional 51 putative orthogroups (POGs) in a re-sequencing data set from 262 barley genotypes and landraces. Whereas the sequences of some POGs are highly conserved across hundreds of barley accessions, the sequences of others are much more variable. High sequence variation strongly correlates with genomic location - the most variable genes are found in a cluster on chromosome 1H. A much higher likelihood of diversifying selection was found for genes within this cluster than for genes present as singlets. This work includes a comprehensive analysis of the patterns of intraspecific variation of RFL genes. The RFL sequences characterised in this study will be useful for the development of new markers for fertility restoration loci.
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Affiliation(s)
- Joanna Melonek
- ARC Centre of Excellence in Plant Energy BiologySchool of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Ruonan Zhou
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)SeelandGermany
| | - Philipp E. Bayer
- School of Biological SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - David Edwards
- School of Biological SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)SeelandGermany
- School of Agriculture and EnvironmentUniversity of Western AustraliaCrawleyWAAustralia
| | - Ian Small
- ARC Centre of Excellence in Plant Energy BiologySchool of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
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9
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Kim YJ, Zhang D. Molecular Control of Male Fertility for Crop Hybrid Breeding. TRENDS IN PLANT SCIENCE 2018; 23:53-65. [PMID: 29126789 DOI: 10.1016/j.tplants.2017.10.001] [Citation(s) in RCA: 148] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 10/17/2017] [Accepted: 10/18/2017] [Indexed: 05/22/2023]
Abstract
In many plant species, male-sterile female lines with cytoplasmic male sterility (CMS) or nuclear-controlled environment-sensitive genic male sterility (EGMS) have long been used to efficiently produce hybrids that harness hybrid vigor or heterosis. However, the underlying molecular mechanisms for these applications have only recently been uncovered in a few species. We provide here an update on the understanding of cytoplasmic-nuclear communication based on the discovery of mitochondrial CMS genes and their corresponding nuclear fertility determinants. Recent findings that uncover diverse mechanisms such as epigenetic, transcriptional, and post-transcriptional controls of EGMS by temperature and photoperiod signals are also reviewed. Furthermore, translational research that applies basic knowledge of plant male fertility control to hybrid seed production practice is highlighted.
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Affiliation(s)
- Yu-Jin Kim
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Department of Oriental Medicinal Biotechnology, College of Life Science, Kyung Hee University, Yongin 446-701, South Korea
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; School of Agriculture, Food, and Wine, University of Adelaide, South Australia 5064, Australia.
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10
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Hackauf B, Bauer E, Korzun V, Miedaner T. Fine mapping of the restorer gene Rfp3 from an Iranian primitive rye (Secale cereale L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1179-1189. [PMID: 28315925 DOI: 10.1007/s00122-017-2879-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 02/13/2017] [Indexed: 06/06/2023]
Abstract
A comparative genetics approach allowed to precisely determine the map position of the restorer gene Rfp3 in rye and revealed that Rfp3 and the restorer gene Rfm1 in barley reside at different positions in a syntenic 4RL/6HS segment. Cytoplasmic male sterility (CMS) is a reliable and striking genetic mechanism for hybrid seed production. Breeding of CMS-based hybrids in cereals requires the use of effective restorer genes as an indispensable pre-requisite. We report on the fine mapping of a restorer gene for the Pampa cytoplasm in winter rye that has been tapped from the Iranian primitive rye population Altevogt 14160. For this purpose, we have mapped 41 gene-derived markers to a 38.8 cM segment in the distal part of the long arm of chromosome 4R, which carries the restorer gene. Male fertility restoration was comprehensively analyzed in progenies of crosses between a male-sterile tester genotype and 21 recombinant as well as six non-recombinant BC4S2 lines. This approach allowed us to validate the position of this restorer gene, which we have designated Rfp3, on chromosome 4RL. Rfp3 was mapped within a 2.5 cM interval and cosegregated with the EST-derived marker c28385. The gene-derived conserved ortholog set (COS) markers enabled us to investigate the orthology of restorer genes originating from different genetic resources of rye as well as barley. The observed localization of Rfp3 and Rfm1 in a syntenic 4RL/6HS segment asks for further efforts towards cloning of both restorer genes as an option to study the mechanisms of male sterility and fertility restoration in cereals.
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Affiliation(s)
- Bernd Hackauf
- Institute for Breeding Research on Agricultural Crops, Julius Kühn-Institut, Rudolf-Schick-Platz 3a, 18190, Groß Lüsewitz, Germany.
| | - Eva Bauer
- Plant Breeding, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354, Freising, Germany
| | - Viktor Korzun
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Straße 5, 29303, Bergen, Germany
| | - Thomas Miedaner
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstr. 21, 70599, Stuttgart, Germany
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Sykes T, Yates S, Nagy I, Asp T, Small I, Studer B. In Silico Identification of Candidate Genes for Fertility Restoration in Cytoplasmic Male Sterile Perennial Ryegrass (Lolium perenne L.). Genome Biol Evol 2017; 9:351-362. [PMID: 26951780 PMCID: PMC5499803 DOI: 10.1093/gbe/evw047] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2016] [Indexed: 12/24/2022] Open
Abstract
Perennial ryegrass (Lolium perenne L.) is widely used for forage production in both permanent and temporary grassland systems. To increase yields in perennial ryegrass, recent breeding efforts have been focused on strategies to more efficiently exploit heterosis by hybrid breeding. Cytoplasmic male sterility (CMS) is a widely applied mechanism to control pollination for commercial hybrid seed production and although CMS systems have been identified in perennial ryegrass, they are yet to be fully characterized. Here, we present a bioinformatics pipeline for efficient identification of candidate restorer of fertility (Rf) genes for CMS. From a high-quality draft of the perennial ryegrass genome, 373 pentatricopeptide repeat (PPR) genes were identified and classified, further identifying 25 restorer of fertility-like PPR (RFL) genes through a combination of DNA sequence clustering and comparison to known Rf genes. This extensive gene family was targeted as the majority of Rf genes in higher plants are RFL genes. These RFL genes were further investigated by phylogenetic analyses, identifying three groups of perennial ryegrass RFLs. These three groups likely represent genomic regions of active RFL generation and identify the probable location of perennial ryegrass PPR-Rf genes. This pipeline allows for the identification of candidate PPR-Rf genes from genomic sequence data and can be used in any plant species. Functional markers for PPR-Rf genes will facilitate map-based cloning of Rf genes and enable the use of CMS as an efficient tool to control pollination for hybrid crop production.
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Affiliation(s)
- Timothy Sykes
- Institute of Agricultural Sciences, Forage Crop Genetics, ETH Zurich, Zurich, Switzerland
| | - Steven Yates
- Institute of Agricultural Sciences, Forage Crop Genetics, ETH Zurich, Zurich, Switzerland
| | - Istvan Nagy
- Department of Molecular Biology and Genetics, Research Centre Flakkebjerg, Aarhus University, Slagelse, Denmark
| | - Torben Asp
- Department of Molecular Biology and Genetics, Research Centre Flakkebjerg, Aarhus University, Slagelse, Denmark
| | - Ian Small
- Plant Energy Biology, ARC Centre of Excellence, the University of Western Australia, Crawley, Western Australia, Australia
| | - Bruno Studer
- Institute of Agricultural Sciences, Forage Crop Genetics, ETH Zurich, Zurich, Switzerland
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12
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Melonek J, Stone JD, Small I. Evolutionary plasticity of restorer-of-fertility-like proteins in rice. Sci Rep 2016; 6:35152. [PMID: 27775031 PMCID: PMC5075784 DOI: 10.1038/srep35152] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 09/26/2016] [Indexed: 11/09/2022] Open
Abstract
Hybrid seed production in rice relies on cytoplasmic male sterility (CMS) induced by specific mitochondrial proteins, whose deleterious effects are suppressed by nuclear Restorer of Fertility (RF) genes. The majority of RF proteins belong to a specific clade of the RNA-binding pentatricopeptide repeat protein family. We have characterised 'restorer-of-fertility-like' (RFL) sequences from 13 Oryza genomes and the Brachypodium distachyon genome. The majority of the RFL sequences are found in genomic clusters located at two or three chromosomal loci with only a minor proportion being present as isolated genes. The RFL genomic cluster located on Oryza chromosome 10, the location of almost all known active rice RF genes, shows extreme variation in structure and gene content between species. We show evidence for homologous recombination events as an efficient mechanism for generating the huge repertoire of RNA sequence recognition motifs within RFL proteins and a major driver of RFL sequence evolution. The RFL sequences identified here will improve our understanding of the molecular basis of CMS and fertility restoration in plants and will accelerate the development of new breeding strategies.
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Affiliation(s)
- Joanna Melonek
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 6009 Crawley, Western Australia
| | - James D Stone
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 6009 Crawley, Western Australia.,Institute of Botany, Czech Academy of Sciences, Zámek 1, Průhonice, 25243 Czech Republic
| | - Ian Small
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 6009 Crawley, Western Australia
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Shavrukov Y. Comparison of SNP and CAPS markers application in genetic research in wheat and barley. BMC PLANT BIOLOGY 2016; 16 Suppl 1:11. [PMID: 26821936 PMCID: PMC4895257 DOI: 10.1186/s12870-015-0689-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
BACKGROUND Barley and bread wheat show large differences in frequencies of Single Nucleotide Polymorphism (SNP) as determined from genome-wide studies. These frequencies have been estimated as 2.4-3 times higher in the entire barley genome than within each diploid genomes of wheat (A, B or D). However, barley SNPs within individual genes occur significantly more frequently than quoted. Differences between wheat and barley are based on the origin and evolutionary history of the species. Bread wheat contains rarer SNPs due to the double genetic 'bottle-neck' created by natural hybridisation and spontaneous polyploidisation. Furthermore, wheat has the lowest level of useful SNP-derived markers while barley is estimated to have the highest level of polymorphism. RESULTS Different strategies are required for the development of suitable molecular markers in these cereal species. For example, SNP markers based on high-throughput technology (Infinium or KASP) are very effective and useful in both barley and bread wheat. In contrast, Cleaved Amplified Polymorphic Sequences (CAPS) are more widely and successfully employed in small-scale experiments with highly polymorphic genetic regions containing multiple SNPs in barley, but not in wheat. However, preliminary 'in silico' search databases for assessing the potential value of SNPs have yet to be developed. CONCLUSIONS This mini-review summarises results supporting the development of different strategies for the application of effective SNP and CAPS markers in wheat and barley.
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Affiliation(s)
- Yuri Shavrukov
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, Australia.
- Department of Biological Sciences, Flinders University, Adelaide, Australia.
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