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Shrestha A, Shim J, Mangat PK, Dhaliwal LK, Sweeney M, Angeles-Shim RB. Genetic Analysis of an F 2 Population Derived from the Cotton Landrace Hopi Identified Novel Loci for Boll Glanding. Int J Mol Sci 2024; 25:7080. [PMID: 39000183 PMCID: PMC11241279 DOI: 10.3390/ijms25137080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 06/16/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024] Open
Abstract
Landraces are an important reservoir of genetic variation that can expand the narrow genetic base of cultivated cotton. In this study, quantitative trait loci (QTL) analysis was conducted using an F2 population developed from crosses between the landrace Hopi and inbred TM-1. A high-density genetic map spanning 2253.11 and 1932.21 cM for the A and D sub-genomes, respectively, with an average marker interval of 1.14 cM, was generated using the CottonSNP63K array. The linkage map showed a strong co-linearity with the physical map of cotton. A total of 21 QTLs were identified, controlling plant height (1), bract type (1), boll number (1), stem color (2), boll pitting (2), fuzz fiber development (2), boll shape (3), boll point (4), and boll glanding (5). In silico analysis of the novel QTLs for boll glanding identified a total of 13 candidate genes. Analysis of tissue-specific expression of the candidate genes suggests roles for the transcription factors bHLH1, MYB2, and ZF1 in gland formation. Comparative sequencing of open reading frames identified early stop codons in all three transcription factors in Hopi. Functional validation of these genes offers avenues to reduce glanding and, consequently, lower gossypol levels in cottonseeds without compromising the defense mechanisms of the plant against biotic stresses.
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Affiliation(s)
- Avinash Shrestha
- Department of Plant and Soil Science, Davis College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX 79409, USA; (A.S.); (J.S.); (P.K.M.); (L.K.D.)
| | - Junghyun Shim
- Department of Plant and Soil Science, Davis College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX 79409, USA; (A.S.); (J.S.); (P.K.M.); (L.K.D.)
| | - Puneet Kaur Mangat
- Department of Plant and Soil Science, Davis College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX 79409, USA; (A.S.); (J.S.); (P.K.M.); (L.K.D.)
| | - Lakhvir Kaur Dhaliwal
- Department of Plant and Soil Science, Davis College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX 79409, USA; (A.S.); (J.S.); (P.K.M.); (L.K.D.)
| | - Megan Sweeney
- BASF Corporation, 407 Davis Drive, Morrisville, NC 27560, USA;
| | - Rosalyn B. Angeles-Shim
- Department of Plant and Soil Science, Davis College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX 79409, USA; (A.S.); (J.S.); (P.K.M.); (L.K.D.)
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Introgression of tsv1 improves tungro disease resistance of a rice variety BRRI dhan71. Sci Rep 2022; 12:18820. [PMID: 36335190 PMCID: PMC9637097 DOI: 10.1038/s41598-022-23413-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022] Open
Abstract
Rice Tungro disease poses a threat to rice production in Asia. Marker assisted backcross breeding is the most feasible approach to address the tungro disease. We targeted to introgress tungro resistance locus tsv1 from Matatag 1 into a popular but tungro susceptible rice variety of Bangladesh, BRRI dhan71. The tsv1 locus was traced using two tightly linked markers RM336 and RM21801, and background genotyping was carried out using 7 K SNPs. A series of three back crosses followed by selfing resulted in identification of plants similar to BRRI dhan71. The background recovery varied at 91-95% with most of the lines having 95%. The disease screening of the lines showed moderate to high level of tungro resistance with a disease index score of ≤ 5. Introgression Lines (ILs) had medium slender grain type, and head rice recovery (59.2%), amylose content (20.1%), gel consistency (40.1 mm) and gelatinization temperature were within the acceptable range. AMMI and Kang's stability analysis based on multi-location data revealed that multiple selected ILs outperformed BRRI dhan71 across the locations. IR144480-2-2-5, IR144483-1-2-4, IR144484-1-2-2 and IR144484-1-2-5 are the most promising lines. These lines will be further evaluated and nominated for varietal testing in Bangladesh.
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Mangat PK, Shim J, Gannaban RB, Singleton JJ, Angeles-Shim RB. Alien introgression and morpho-agronomic characterization of diploid progenies of Solanum lycopersicoides monosomic alien addition lines (MAALs) toward pre-breeding applications in tomato (S. lycopersicum). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1133-1146. [PMID: 33386862 PMCID: PMC7973918 DOI: 10.1007/s00122-020-03758-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 12/19/2020] [Indexed: 06/12/2023]
Abstract
Alien introgressions that were captured in the genome of diploid plants segregating from progenies of monosomic alien addition lines of S. lycopersicoides confer novel phenotypes with commercial and agronomic value in tomato breeding. Solanum lycopersicoides is a wild relative of tomato with a natural adaptation to a wide array of biotic and abiotic challenges. In this study, we identified and characterized diploid plants segregating from the progenies of monosomic alien addition lines (MAALs) of S. lycopersicoides to establish their potential as donors in breeding for target trait improvement in tomato. Molecular genotyping identified 28 of 38 MAAL progenies having the complete chromosome complement of the cultivated tomato parent and limited chromosome introgressions from the wild S. lycopersicoides parent. Analysis of SSR and indel marker profiles identified 34 unique alien introgressions in the 28 MAAL-derived introgression lines (MDILs) in the genetic background of tomato. Conserved patterns of alien introgressions were detected among sibs of MDILs 2, 3, 4 and 8. Across MDILs, a degree of preferential transmission of specific chromosome segments was also observed. Morphologically, the MDILs closely resembled the cultivated tomato more than S. lycopersicoides. The appearance of novel phenotypes in the MDILs that are lacking in the cultivated parent or the source MAALs indicates the capture of novel genetic variation by the diploid introgression lines that can add commercial and agronomic value to tomato. In particular, screening of representative MDILs for drought tolerance at the vegetative stage identified MDIL 2 and MDIL 11III as drought tolerant based on visual scoring. A regulated increase in stomatal conductance of MDIL 2 under drought stress indicates better water use efficiency that allowed it to survive for 7 days under 0% moisture level.
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Affiliation(s)
- Puneet Kaur Mangat
- Department of Plant and Soil Science, College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX, 79409-2122, USA
| | - Junghyun Shim
- Department of Plant and Soil Science, College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX, 79409-2122, USA
| | - Ritchel B Gannaban
- Department of Plant and Soil Science, College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX, 79409-2122, USA
| | - Joshua J Singleton
- Department of Plant and Soil Science, College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX, 79409-2122, USA
| | - Rosalyn B Angeles-Shim
- Department of Plant and Soil Science, College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX, 79409-2122, USA.
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Mangat PK, Gannaban RB, Singleton JJ, Angeles-Shim RB. Development of a PCR-based, genetic marker resource for the tomato-like nightshade relative, Solanum lycopersicoides using whole genome sequence analysis. PLoS One 2020; 15:e0242882. [PMID: 33227039 PMCID: PMC7682897 DOI: 10.1371/journal.pone.0242882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/10/2020] [Indexed: 11/23/2022] Open
Abstract
Solanum lycopersicoides is a wild nightshade relative of tomato with known resistance to a wide range of pests and pathogens, as well as tolerance to cold, drought and salt stress. To effectively utilize S. lycopersicoides as a genetic resource in breeding for tomato improvement, the underlying basis of observable traits in the species needs to be understood. Molecular markers are important tools that can unlock the genetic underpinnings of phenotypic variation in wild crop relatives. Unfortunately, DNA markers that are specific to S. lycopersicoides are limited in number, distribution and polymorphism rate. In this study, we developed a suite of S. lycopersicoides-specific SSR and indel markers by sequencing, building and analyzing a draft assembly of the wild nightshade genome. Mapping of a total of 1.45 Gb of S. lycopersicoides contigs against the tomato reference genome assembled a moderate number of contiguous reads into longer scaffolds. Interrogation of the obtained draft yielded SSR information for more than 55,000 loci in S. lycopersicoides for which more than 35,000 primers pairs were designed. Additionally, indel markers were developed based on sequence alignments between S. lycopersicoides and tomato. Synthesis and experimental validation of 345 primer sets resulted in the amplification of single and multilocus targets in S. lycopersicoides and polymorphic loci between S. lycopersicoides and tomato. Cross-species amplification of the 345 markers in tomato, eggplant, silverleaf nightshade and pepper resulted in varying degrees of transferability that ranged from 55 to 83%. The markers reported in this study significantly expands the genetic marker resource for S. lycopersicoides, as well as for related Solanum spp. for applications in genetics and breeding studies.
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Affiliation(s)
- Puneet Kaur Mangat
- Department of Plant and Soil Science, College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, Texas, United States of America
| | - Ritchel B. Gannaban
- Department of Plant and Soil Science, College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, Texas, United States of America
| | - Joshua J. Singleton
- Department of Plant and Soil Science, College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, Texas, United States of America
| | - Rosalyn B. Angeles-Shim
- Department of Plant and Soil Science, College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, Texas, United States of America
- * E-mail:
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Angeles-Shim RB, Shim J, Vinarao RB, Lapis RS, Singleton JJ. A novel locus from the wild allotetraploid rice species Oryza latifolia Desv. confers bacterial blight (Xanthomonas oryzae pv. oryzae) resistance in rice (O. sativa). PLoS One 2020; 15:e0229155. [PMID: 32084193 PMCID: PMC7034821 DOI: 10.1371/journal.pone.0229155] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/30/2020] [Indexed: 11/19/2022] Open
Abstract
Bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major limiting factor to rice productivity worldwide. Genetic control through the identification of novel sources of bacterial blight resistance and their utilization in resistance breeding remains the most effective and economical strategy to manage the disease. Here we report the identification of a novel locus from the wild Oryza species, Oryza latifolia, conferring a race-specific resistance to Philippine Xoo race 9A (PXO339). The locus was identified from two introgression lines i.e. WH12-2252 and WH12-2256 that segregated from O. latifolia monosomic alien addition lines (MAALs). The discrete segregation ratio of susceptible and resistant phenotypes in the F2 (χ2[3:1] = 0.22 at p>0.05) and F3 (χ2[3:1] = 0.36 at p>0.05) populations indicates that PXO339 resistance in the MAAL-derived introgression lines (MDILs) is controlled by a single, recessive gene. Genotyping of a total of 216 F2, 1130 F3 and 288 F4 plants derived from crossing either of the MDILs with the recurrent parent used to generate the MAALs narrowed the candidate region to a 1,817 kb locus that extends from 10,425 to 12,266 kb in chromosome 12. Putative candidate genes that were identified by data mining and comparative sequence analysis can provide targets for further studies on mapping and cloning of the causal gene for PXO339 resistance in the MDILs. To our knowledge, this is the first report of a genetic locus from the allotetraploid wild rice, O. latifolia conferring race-specific resistance to bacterial blight.
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Affiliation(s)
| | - Junghyun Shim
- Plant Breeding Division, International Rice Research Institute, Manila, Philippines
| | - Ricky B. Vinarao
- Plant Breeding Division, International Rice Research Institute, Manila, Philippines
| | - Ruby S. Lapis
- Plant Breeding Division, International Rice Research Institute, Manila, Philippines
| | - Joshua J. Singleton
- Plant Breeding Division, International Rice Research Institute, Manila, Philippines
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Arbelaez JD, Tandayu E, Reveche MY, Jarana A, van Rogen P, Sandager L, Stolt P, Ng E, Varshney RK, Kretzschmar T, Cobb J. Methodology: ssb- MASS: a single seed-based sampling strategy for marker-assisted selection in rice. PLANT METHODS 2019; 15:78. [PMID: 31367224 PMCID: PMC6652012 DOI: 10.1186/s13007-019-0464-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/16/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Integrated breeding approaches such as combining marker-assisted selection and rapid line fixation through single-seed-descent, can effectively increase the frequency of desirable alleles in a breeding program and increase the rate of genetic gain for quantitative traits by shortening the breeding cycle. However, with most genotyping being outsourced to 3rd party service providers' nowadays, sampling has become the bottleneck for many breeding programs. While seed-chipping as prevailed as an automatable seed sampling protocol in many species, the symmetry of rice seeds makes this solution as laborious and costly as sampling leaf tissue. The aim of this study is to develop, validate and deploy a single seed sampling strategy for marker-assisted selection of fixed lines in rice that is more efficient, cost-effective and convenient compared to leaf-based sampling protocols without compromising the accuracy of the marker-assisted selection results. RESULTS Evaluations replicated across accessions and markers showed that a single rice seed is sufficient to generate enough DNA (7-8 ng/μL) to run at least ten PCR trait-markers suitable for marker-assisted selection strategies in rice. The DNA quantity and quality extracted from single seeds from fixed lines (F6) with different physical and/or chemical properties were not significantly different. Nor were there significant differences between single seeds collected 15 days after panicle initiation compared to those harvested at maturity. A large-scale comparison between single seed and leaf-based methodologies showed not only high levels of genotypic concordance between both protocols (~ 99%) but also higher SNP call rates in single seed (99.24% vs. 97.5% in leaf). A cost-benefit analysis showed that this single seed sampling strategy decreased the cost of sampling fourfold. An advantage of this approach is that desirable genotypes can be selected before investing in planting activities reducing the cost associated with field operations. CONCLUSION This study reports the development of a cost-effective and simple single seed genotyping strategy that facilitates the adoption and deployment of marker-assisted selection strategies in rice. This will allow breeders to increase the frequency of favorable alleles and combine rapid generation advancement techniques much more cost-effectively accelerating the process and efficiency of parental selection and varietal development.
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Affiliation(s)
- Juan David Arbelaez
- International Rice Research Institute, Metro Manila, DAPO Box 7777, Los Baños, 1301 Philippines
| | - Erwin Tandayu
- International Rice Research Institute, Metro Manila, DAPO Box 7777, Los Baños, 1301 Philippines
- Intertek - AgriTech, 2-230-53 Alnarp, Elevenborgsvägen Sweden
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana India
| | - Maria Ymber Reveche
- International Rice Research Institute, Metro Manila, DAPO Box 7777, Los Baños, 1301 Philippines
| | - Annalhea Jarana
- International Rice Research Institute, Metro Manila, DAPO Box 7777, Los Baños, 1301 Philippines
| | - Petra van Rogen
- Intertek - AgriTech, 2-230-53 Alnarp, Elevenborgsvägen Sweden
| | - Line Sandager
- Intertek - AgriTech, 2-230-53 Alnarp, Elevenborgsvägen Sweden
| | - Patrik Stolt
- Intertek - AgriTech, 2-230-53 Alnarp, Elevenborgsvägen Sweden
| | - Enghwa Ng
- International Rice Research Institute, Metro Manila, DAPO Box 7777, Los Baños, 1301 Philippines
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana India
| | - Tobias Kretzschmar
- Southern Cross Plant Science, Southern Cross University, PO Box 157, Lismore, NSW 2480 Australia
| | - Joshua Cobb
- International Rice Research Institute, Metro Manila, DAPO Box 7777, Los Baños, 1301 Philippines
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Srilatha P, Yousuf F, Methre R, Vishnukiran T, Agarwal S, Poli Y, Raghurami Reddy M, Vidyasagar B, Shanker C, Krishnaveni D, Triveni S, Brajendra, Praveen S, Balachandran S, Subrahmanyam D, Mangrauthia SK. Physical interaction of RTBV ORFI with D1 protein of Oryza sativa and Fe/Zn homeostasis play a key role in symptoms development during rice tungro disease to facilitate the insect mediated virus transmission. Virology 2019; 526:117-124. [DOI: 10.1016/j.virol.2018.10.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 10/10/2018] [Accepted: 10/11/2018] [Indexed: 10/28/2022]
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