1
|
Choe ME, Kim JY, Syed Nabi RB, Han SI, Cho KS. Development of InDels markers for the identification of cytoplasmic male sterility in Sorghum by complete chloroplast genome sequences analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1188149. [PMID: 37528970 PMCID: PMC10388542 DOI: 10.3389/fpls.2023.1188149] [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: 03/17/2023] [Accepted: 06/26/2023] [Indexed: 08/03/2023]
Abstract
Cytoplasmic male sterility (CMS) is predominantly used for F1 hybrid breeding and seed production in Sorghum. DNA markers to distinguish between normal fertile (CMS-N) and sterile (CMS-S) male cytoplasm can facilitate F1 hybrid cultivar development in Sorghum breeding programs. In this study, the complete chloroplast (cp) genome sequences of CMS-S and Korean Sorghum cultivars were obtained using next-generation sequencing. The de novo assembled genome size of ATx623, the CMS-S line of the chloroplast, was 140,644bp. When compared to the CMS-S and CMS-N cp genomes, 19 single nucleotide polymorphisms (SNPs) and 142 insertions and deletions (InDels) were identified, which can be used for marker development for breeding, population genetics, and evolution studies. Two InDel markers with sizes greater than 20 bp were developed to distinguish cytotypes based on the copy number variation of lengths as 28 and 22 bp tandem repeats, respectively. Using the newly developed InDel markers with five pairs of CMS-S and their near isogenic maintainer line, we were able to easily identify their respective cytotypes. The InDel markers were further examined and applied to 1,104 plants from six Korean Sorghum cultivars to identify variant cytotypes. Additionally, the phylogenetic analysis of seven Sorghum species with complete cp genome sequences, including wild species, indicated that CMS-S and CMS-N contained Milo and Kafir cytotypes that might be hybridized from S. propinquum and S. sudanese, respectively. This study can facilitate F1 hybrid cultivar development by providing breeders with reliable tools for marker-assisted selection to breed desirable Sorghum varieties.
Collapse
|
2
|
Molecular Breeding of Sorghum bicolor, A Novel Energy Crop. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 321:221-57. [PMID: 26811289 DOI: 10.1016/bs.ircmb.2015.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Currently, molecular breeding is regarded as an important tool for the improvement of many crop species. However, in sorghum, recently heralded as an important bioenergy crop, progress in this field has been relatively slow and limited. In this review, we present existing efforts targeted at genetic characterization of sorghum mutants. We also comprehensively review the different attempts made toward the isolation of genes involved in agronomically important traits, including the dissection of some sorghum quantitative trait loci (QTLs). We also explore the current status of the use of transgenic techniques in sorghum, which should be crucial for advancing sorghum molecular breeding. Through this report, we provide a useful benchmark to help assess how much more sorghum genomics and molecular breeding could be improved.
Collapse
|
3
|
Praveen M, Anurag Uttam G, Suneetha N, Umakanth A, Patil JV, Madhusudhana R. Inheritance and molecular mapping of Rf6 locus with pollen fertility restoration ability on A1 and A2 cytoplasms in sorghum. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 238:73-80. [PMID: 26259176 DOI: 10.1016/j.plantsci.2015.05.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 05/19/2015] [Accepted: 05/30/2015] [Indexed: 05/20/2023]
Abstract
Of the several male sterility cytoplasms available as an alternative to the widely exploited A1 (milo) cytoplasm in sorghum, A2 is more suitable for commercial exploitation. Diversification of genetic and cytoplasmic base of hybrids involving A2 cytoplasm necessitates mapping of fertility restorer (Rf) genes for use in marker-assisted restorer development. We mapped a major male fertility restoration locus on sorghum chromosome 4 tightly linked with SSR markers, SB2387 and SB2388. This new fertility locus, Rf6, was able to restore male fertility on both A1 and A2 cytoplasms. Analysis of the genomic region around the Rf6 locus identified six genes including a pentatricopeptide repeat (PPR) gene, Sobic.004G004100. With its similar restoration ability to Rf1, Rf2 and Rf5 loci in sorghum, it is most likely that the Rf6 is a member of the PPR gene family, and the PPR gene Sobic.004G004100 could be a candidate for fertility restoration on A1 and A2 cytoplasms.
Collapse
Affiliation(s)
- M Praveen
- Marker-assisted Selection Laboratory, ICAR-Indian Institute of Millet Research (IIMR), Rajendranagar, Hyderabad 500 030, India
| | - G Anurag Uttam
- Marker-assisted Selection Laboratory, ICAR-Indian Institute of Millet Research (IIMR), Rajendranagar, Hyderabad 500 030, India
| | - N Suneetha
- Joginpally B.R Engineering College, Moinabad, Hyderabad, India
| | - Av Umakanth
- Marker-assisted Selection Laboratory, ICAR-Indian Institute of Millet Research (IIMR), Rajendranagar, Hyderabad 500 030, India
| | - J V Patil
- Marker-assisted Selection Laboratory, ICAR-Indian Institute of Millet Research (IIMR), Rajendranagar, Hyderabad 500 030, India
| | - R Madhusudhana
- Marker-assisted Selection Laboratory, ICAR-Indian Institute of Millet Research (IIMR), Rajendranagar, Hyderabad 500 030, India.
| |
Collapse
|
4
|
Li S, Liu G, Chen Z, Wang Y, Li P, Hua J. Construction and initial analysis of five Fosmid libraries of mitochondrial genomes of cotton (Gossypium). ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s11434-013-5962-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
5
|
Kumar AA, Reddy BVS, Sharma HC, Hash CT, Rao PS, Ramaiah B, Reddy PS. Recent Advances in Sorghum Genetic Enhancement Research at ICRISAT. ACTA ACUST UNITED AC 2011. [DOI: 10.4236/ajps.2011.24070] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
6
|
Dwivedi S, Perotti E, Ortiz R. Towards molecular breeding of reproductive traits in cereal crops. PLANT BIOTECHNOLOGY JOURNAL 2008; 6:529-559. [PMID: 18507792 DOI: 10.1111/j.1467-7652.2008.00343.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The transition from vegetative to reproductive phase, flowering per se, floral organ development, panicle structure and morphology, meiosis, pollination and fertilization, cytoplasmic male sterility (CMS) and fertility restoration, and grain development are the main reproductive traits. Unlocking their genetic insights will enable plant breeders to manipulate these traits in cereal germplasm enhancement. Multiple genes or quantitative trait loci (QTLs) affecting flowering (phase transition, photoperiod and vernalization, flowering per se), panicle morphology and grain development have been cloned, and gene expression research has provided new information about the nature of complex genetic networks involved in the expression of these traits. Molecular biology is also facilitating the identification of diverse CMS sources in hybrid breeding. Few Rf (fertility restorer) genes have been cloned in maize, rice and sorghum. DNA markers are now used to assess the genetic purity of hybrids and their parental lines, and to pyramid Rf or tms (thermosensitive male sterility) genes in rice. Transgene(s) can be used to create de novo CMS trait in cereals. The understanding of reproductive biology facilitated by functional genomics will allow a better manipulation of genes by crop breeders and their potential use across species through genetic transformation.
Collapse
Affiliation(s)
- Sangam Dwivedi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Andhra Pradesh, India.
| | | | | |
Collapse
|
7
|
Kempken F, Pring D. Plant Breeding: Male Sterility in Higher Plants - Fundamentals and Applications. ACTA ACUST UNITED AC 1999. [DOI: 10.1007/978-3-642-59940-8_6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
|
8
|
Tang HV, Chang R, Pring DR. Cosegregation of single genes associated with fertility restoration and transcript processing of sorghum mitochondrial orf107 and urf209. Genetics 1998; 150:383-91. [PMID: 9725854 PMCID: PMC1460301 DOI: 10.1093/genetics/150.1.383] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Defective nuclear-cytoplasmic interactions leading to aberrant microgametogenesis in sorghum carrying the IS1112C male-sterile cytoplasm occur very late in pollen maturation. Amelioration of this condition, the restoration of pollen viability, involves a novel two-gene gametophytic system, wherein genes designated Rf3 and Rf4 are required for viability of individual gametes. Rf3 is tightly linked to, or represents, a single gene that regulates a transcript processing activity that cleaves transcripts of orf107, a chimeric mitochondrial open reading frame specific to IS1112C. The mitochondrial gene urf209 is also subject to nucleus-specific enhanced transcript processing, 5' to the gene, conferred by a single dominant gene designated Mmt1. Examinations of transcript patterns in F2 and two backcross populations indicated cosegregation of the augmented orf107 and urf209 processing activities in IS1112C. Several sorghum lines that do not restore fertility or confer orf107 transcript processing do exhibit urf209 transcript processing, indicating that the activities are distinguishable. We conclude that the nuclear gene(s) conferring enhanced orf107 and urf209 processing activities are tightly linked in IS1112C. Alternatively, the similarity in apparent regulatory action of the genes may indicate allelic differences wherein the IS1112C Rf3 allele may differ from alleles of maintainer lines by the capability to regulate both orf107 and urf209 processing activities.
Collapse
Affiliation(s)
- H V Tang
- Crop Genetics and Environment Research Unit, U.S. Department of Agriculture-Agricultural Research Service, and Department of Plant Pathology and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, 32611, USA
| | | | | |
Collapse
|
9
|
Howad W, Kempken F. Cell type-specific loss of atp6 RNA editing in cytoplasmic male sterile Sorghum bicolor. Proc Natl Acad Sci U S A 1997; 94:11090-5. [PMID: 9380764 PMCID: PMC23623 DOI: 10.1073/pnas.94.20.11090] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
RNA editing and cytoplasmic male sterility are two important phenomena in higher plant mitochondria. To determine whether correlations might exist between the two, RNA editing in different tissues of Sorghum bicolor was compared employing reverse transcription-PCR and subsequent sequence analysis. In etiolated shoots, RNA editing of transcripts of plant mitochondrial atp6, atp9, nad3, nad4, and rps12 genes was identical among fertile or cytoplasmic male sterile plants. We then established a protocol for mitochondrial RNA isolation from plant anthers and pollen to include in these studies. Whereas RNA editing of atp9, nad3, nad4, and rps12 transcripts in anthers was similar to etiolated shoots, mitochondrial atp6 RNA editing was strongly reduced in anthers of the A3Tx398 male sterile line of S. bicolor. atp6 transcripts of wheat and selected plastid transcripts in S. bicolor showed normal RNA editing, indicating that loss of atp6 RNA editing is specific for cytoplasmic male sterility S. bicolor mitochondria. Restoration of fertility in F1 and F2 lines correlated with an increase in RNA editing of atp6 transcripts. Our data suggest that loss of atp6 RNA editing contributes to or causes cytoplasmic male sterility in S. bicolor. Further analysis of the mechanism of cell type-specific loss of atp6 RNA editing activity may advance our understanding of the mechanism of RNA editing.
Collapse
Affiliation(s)
- W Howad
- Lehrstuhl für Allgemeine Botanik, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | | |
Collapse
|
10
|
Sane AP, Nath P, Sane PV. Cytoplasmic male sterility in sorghum: Organization and expression of mitochondrial genes in Indian CMS cytoplasms. J Genet 1996. [DOI: 10.1007/bf02931758] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
11
|
Cui YX, Xu GW, Magill CW, Schertz KF, Hart GE. RFLP-based assay of Sorghum bicolor (L.) Moench genetic diversity. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1995; 90:787-796. [PMID: 24172920 DOI: 10.1007/bf00222013] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/1994] [Accepted: 10/18/1994] [Indexed: 06/02/2023]
Abstract
Sixty-two single-copy sorghum DNA clones were used to compare restriction fragment patterns of 53 sorghum accessions from Africa, Asia and the United States. Included were accessions from five morphological races of the cultivated subspecies bicolor, and four races of the wild subspecies verticilliflorum. From two to twelve alleles were detected with each probe. There was greater nuclear diversity in the wild subspecies (255 alleles in ten accessions) than in the domestic accessions (236 alleles in 37 accessions). Overall, 204 of the 340 alleles (60%) that were detected occurred in both subspecies. Phylogenetic analysis using parsimony separated the subspecies into separate clusters, with one group of intermediate accessions. Though exceptions were common, especially for the race bicolor, accessions classified as the same morphological race tended to group together on the basis of RFLP similarities. Selection for traits such as forage quality may have led to accessions genetically more similar to other races being classified as bicolors, which have a loose, small-grained panicle similar to wild races. Population statistics, calculated using four nuclear and four cytoplasmic probes that detect two alleles each, revealed a low but significant amount of heterozygosity, and showed little differentiation in alleles in the wild and cultivated subspecies. Outcrossing with foreign pollen appears to have been more important than migration via seed dispersal as a mechanism for gene flow between the wild and domestic accessions included in this study.
Collapse
Affiliation(s)
- Y X Cui
- Department of Soil and Crop Sciences, Texas A&M University, 77843, College Station, Texas, USA
| | | | | | | | | |
Collapse
|