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Schoonmaker AN, Hulse-Kemp AM, Youngblood RC, Rahmat Z, Atif Iqbal M, Rahman MU, Kochan KJ, Scheffler BE, Scheffler JA. Detecting Cotton Leaf Curl Virus Resistance Quantitative Trait Loci in Gossypium hirsutum and iCottonQTL a New R/Shiny App to Streamline Genetic Mapping. Plants (Basel) 2023; 12:1153. [PMID: 36904013 PMCID: PMC10005503 DOI: 10.3390/plants12051153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/21/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Cotton leaf curl virus (CLCuV) causes devastating losses to fiber production in Central Asia. Viral spread across Asia in the last decade is causing concern that the virus will spread further before resistant varieties can be bred. Current development depends on screening each generation under disease pressure in a country where the disease is endemic. We utilized quantitative trait loci (QTL) mapping in four crosses with different sources of resistance to identify single nucleotide polymorphism (SNP) markers associated with the resistance trait to allow development of varieties without the need for field screening every generation. To assist in the analysis of multiple populations, a new publicly available R/Shiny App was developed to streamline genetic mapping using SNP arrays and to also provide an easy method to convert and deposit genetic data into the CottonGen database. Results identified several QTL from each cross, indicating possible multiple modes of resistance. Multiple sources of resistance would provide several genetic routes to combat the virus as it evolves over time. Kompetitive allele specific PCR (KASP) markers were developed and validated for a subset of QTL, which can be used in further development of CLCuV-resistant cotton lines.
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Affiliation(s)
- Ashley N. Schoonmaker
- Bioinformatics Graduate Program, North Carolina State University, Raleigh, NC 27695, USA
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Amanda M. Hulse-Kemp
- Bioinformatics Graduate Program, North Carolina State University, Raleigh, NC 27695, USA
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA
- USDA Agricultural Research Service, Genomics and Bioinformatics Research Unit, Raleigh, NC 27695, USA
| | - Ramey C. Youngblood
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS 39762, USA
| | - Zainab Rahmat
- Plant Genomics and Molecular Breeding Laboratory, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences, (NIBGE-C, PIEAS), Faisalabad 38000, Punjab, Pakistan
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Muhammad Atif Iqbal
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Mehboob-ur Rahman
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Kelli J. Kochan
- Institute for Genome Sciences and Society, Texas A&M University, College Station, TX 77843, USA
| | - Brian E. Scheffler
- USDA Agricultural Research Service, Genomics and Bioinformatics Research Unit, Stoneville, MS 38776, USA
| | - Jodi A. Scheffler
- USDA Agricultural Research Service, Crop Genetics Research Unit, Stoneville, MS 38776, USA
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Aslam MQ, Naqvi RZ, Zaidi SSEA, Asif M, Akhter KP, Scheffler BE, Scheffler JA, Liu SS, Amin I, Mansoor S. Analysis of a tetraploid cotton line Mac7 transcriptome reveals mechanisms underlying resistance against the whitefly Bemisia tabaci. Gene 2022; 820:146200. [PMID: 35131368 DOI: 10.1016/j.gene.2022.146200] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 12/14/2021] [Accepted: 01/13/2022] [Indexed: 01/09/2023]
Abstract
Whitefly inflicts both direct and indirect losses to cotton crop. Whitefly resistant cotton germplasm is a high priority and considered among the best possible solutions to mitigate this issue. In this study, we evaluated cotton leaf curl disease (CLCuD) resistant cotton line Mac7 under whitefly stress. Furthermore, we utilized the already available transcriptome data of Mac7 concerning whitefly stress to elucidate associated mechanisms and identify functionally important genes in cotton. In transcriptomic data analysis, differentially expressed genes (DEGs) were found involved in complex relay pathways, activated on whitefly exposure. The response implicates signalling through resistance genes (R-genes), MAPK, ROS, VQs or RLKs, transcription factors, which leads to the activation of defence responses including, Ca2+messengers, phytohormonal cross-talk, gossypol, flavonoids, PhasiRNA and susceptibility genes (S-genes). The qRT-PCR assay of 10 functionally important genes also showed their involvement in differential responses at 24 and 48 h post whitefly infestation. Briefly, our study helps in understanding the resistant nature of Mac7 under whitefly stress.
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Affiliation(s)
- Muhammad Qasim Aslam
- National Institute for Biotechnology and Genetic Engineering, Constituent College of PIEAS, Faisalabad, Pakistan
| | - Rubab Zahra Naqvi
- National Institute for Biotechnology and Genetic Engineering, Constituent College of PIEAS, Faisalabad, Pakistan
| | | | - Muhammad Asif
- National Institute for Biotechnology and Genetic Engineering, Constituent College of PIEAS, Faisalabad, Pakistan
| | | | - Brian E Scheffler
- Genomics and Bioinformatics Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), 141 Experimental Station Road, Stoneville, MS, United States
| | - Jodi A Scheffler
- Crop Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), 141 Experimental Station Road, Stoneville, MS, United States
| | - Shu-Sheng Liu
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Imran Amin
- National Institute for Biotechnology and Genetic Engineering, Constituent College of PIEAS, Faisalabad, Pakistan
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering, Constituent College of PIEAS, Faisalabad, Pakistan.
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Restrepo-Montoya D, Hulse-Kemp AM, Scheffler JA, Haigler CH, Hinze LL, Love J, Percy RG, Jones DC, Frelichowski J. Leveraging National Germplasm Collections to Determine Significantly Associated Categorical Traits in Crops: Upland and Pima Cotton as a Case Study. Front Plant Sci 2022; 13:837038. [PMID: 35557715 PMCID: PMC9087864 DOI: 10.3389/fpls.2022.837038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/21/2022] [Indexed: 06/15/2023]
Abstract
Observable qualitative traits are relatively stable across environments and are commonly used to evaluate crop genetic diversity. Recently, molecular markers have largely superseded describing phenotypes in diversity surveys. However, qualitative descriptors are useful in cataloging germplasm collections and for describing new germplasm in patents, publications, and/or the Plant Variety Protection (PVP) system. This research focused on the comparative analysis of standardized cotton traits as represented within the National Cotton Germplasm Collection (NCGC). The cotton traits are named by 'descriptors' that have non-numerical sub-categories (descriptor states) reflecting the details of how each trait manifests or is absent in the plant. We statistically assessed selected accessions from three major groups of Gossypium as defined by the NCGC curator: (1) "Stoneville accessions (SA)," containing mainly Upland cotton (Gossypium hirsutum) cultivars; (2) "Texas accessions (TEX)," containing mainly G. hirsutum landraces; and (3) Gossypium barbadense (Gb), containing cultivars or landraces of Pima cotton (Gossypium barbadense). For 33 cotton descriptors we: (a) revealed distributions of character states for each descriptor within each group; (b) analyzed bivariate associations between paired descriptors; and (c) clustered accessions based on their descriptors. The fewest significant associations between descriptors occurred in the SA dataset, likely reflecting extensive breeding for cultivar development. In contrast, the TEX and Gb datasets showed a higher number of significant associations between descriptors, likely correlating with less impact from breeding efforts. Three significant bivariate associations were identified for all three groups, bract nectaries:boll nectaries, leaf hair:stem hair, and lint color:seed fuzz color. Unsupervised clustering analysis recapitulated the species labels for about 97% of the accessions. Unexpected clustering results indicated accessions that may benefit from potential further investigation. In the future, the significant associations between standardized descriptors can be used by curators to determine whether new exotic/unusual accessions most closely resemble Upland or Pima cotton. In addition, the study shows how existing descriptors for large germplasm datasets can be useful to inform downstream goals in breeding and research, such as identifying rare individuals with specific trait combinations and targeting breakdown of remaining trait associations through breeding, thus demonstrating the utility of the analytical methods employed in categorizing germplasm diversity within the collection.
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Affiliation(s)
- Daniel Restrepo-Montoya
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
| | - Amanda M. Hulse-Kemp
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
- Genomics and Bioinformatics Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Raleigh, NC, United States
| | - Jodi A. Scheffler
- Crop Genetics Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Stoneville, MS, United States
| | - Candace H. Haigler
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Lori L. Hinze
- Crop Germplasm Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), College Station, TX, United States
| | - Janna Love
- Crop Germplasm Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), College Station, TX, United States
| | - Richard G. Percy
- Crop Germplasm Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), College Station, TX, United States
| | | | - James Frelichowski
- Crop Germplasm Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), College Station, TX, United States
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Bellaloui N, Saha S, Tonos JL, Scheffler JA, Jenkins JN, McCarty JC, Stelly DM. Effects of Interspecific Chromosome Substitution in Upland Cotton on Cottonseed Macronutrients. Plants (Basel) 2021; 10:plants10061158. [PMID: 34200224 PMCID: PMC8226993 DOI: 10.3390/plants10061158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 05/30/2021] [Accepted: 06/01/2021] [Indexed: 11/16/2022]
Abstract
Nutrients, including macronutrients such as Ca, P, K, and Mg, are essential for crop production and seed quality, and for human and animal nutrition and health. Macronutrient deficiencies in soil lead to poor crop nutritional qualities and a low level of macronutrients in cottonseed meal-based products, leading to malnutrition. Therefore, the discovery of novel germplasm with a high level of macronutrients or significant variability in the macronutrient content of crop seeds is critical. To our knowledge, there is no information available on the effects of chromosome or chromosome arm substitution on cottonseed macronutrient content. The objective of this study was to evaluate the effects of chromosome or chromosome arm substitution on the variability and content of the cottonseed macronutrients Ca, K, Mg, N, P, and S in chromosome substitution lines (CS). Nine chromosome substitution lines were grown in two-field experiments at two locations in 2013 in South Carolina, USA, and in 2014 in Mississippi, USA. The controls used were TM-1, the recurrent parent of the CS line, and the cultivar AM UA48. The results showed major variability in macronutrients among CS lines and between CS lines and controls. For example, in South Carolina, the mean values showed that five CS lines (CS-T02, CS-T04, CS-T08sh, CS-B02, and CS-B04) had higher Ca level in seed than controls. Ca levels in these CS lines varied from 1.88 to 2.63 g kg-1 compared with 1.81 and 1.72 g kg-1 for TM-1 and AMUA48, respectively, with CS-T04 having the highest Ca concentration. CS-M08sh exhibited the highest K concentration (14.50 g kg-1), an increase of 29% and 49% over TM-1 and AM UA48, respectively. Other CS lines had higher Mg, P, and S than the controls. A similar trend was found at the MS location. This research demonstrated that chromosome substitution resulted in higher seed macronutrients in some CS lines, and these CS lines with a higher content of macronutrients can be used as a genetic tool towards the identification of desired seed nutrition traits. Also, the CS lines with higher desired macronutrients can be used as parents to breed for improved nutritional quality in Upland cotton, Gossypium hirsutum L., through improvement by the interspecific introgression of desired seed nutrient traits such as Ca, K, P, S, and N. The positive and significant (p ≤ 0.0001) correlation of P with Ca, P with Mg, S with P, and S with N will aid in understanding the relationships between nutrients to improve the fertilizer management program and maintain higher cottonseed nutrient content.
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Affiliation(s)
- Nacer Bellaloui
- Crop Genetics Research Unit, USDA, Agriculture Research Service, 141 Experiment Station Road, Stoneville, MS 38776, USA; (J.L.T.); (J.A.S.)
- Correspondence:
| | - Sukumar Saha
- Genetics and Sustainable Agriculture Research Unit, USDA, Agriculture Research Service, Starkville, MS 39762, USA; (S.S.); (J.N.J.); (J.C.M.)
| | - Jennifer L. Tonos
- Crop Genetics Research Unit, USDA, Agriculture Research Service, 141 Experiment Station Road, Stoneville, MS 38776, USA; (J.L.T.); (J.A.S.)
| | - Jodi A. Scheffler
- Crop Genetics Research Unit, USDA, Agriculture Research Service, 141 Experiment Station Road, Stoneville, MS 38776, USA; (J.L.T.); (J.A.S.)
| | - Johnie N. Jenkins
- Genetics and Sustainable Agriculture Research Unit, USDA, Agriculture Research Service, Starkville, MS 39762, USA; (S.S.); (J.N.J.); (J.C.M.)
| | - Jack C. McCarty
- Genetics and Sustainable Agriculture Research Unit, USDA, Agriculture Research Service, Starkville, MS 39762, USA; (S.S.); (J.N.J.); (J.C.M.)
| | - David M. Stelly
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA;
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Bellaloui N, Saha S, Tonos JL, Scheffler JA, Jenkins JN, McCarty JC, Stelly DM. Effects of Interspecific Chromosome Substitution in Upland Cotton on Cottonseed Micronutrients. Plants (Basel) 2020; 9:E1081. [PMID: 32842514 PMCID: PMC7569972 DOI: 10.3390/plants9091081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 08/16/2020] [Accepted: 08/18/2020] [Indexed: 11/16/2022]
Abstract
Micronutrients are essential for plant growth and development, and important for human health nutrition and livestock feed. Therefore, the discovery of novel germplasm with significant variability or higher micronutrients content in crop seeds is critical. Currently, there is no information available on the effects of chromosome or chromosome arm substitution in cotton on cottonseed micronutrients. Thus, the objective of this study was to evaluate the effects of chromosome or chromosome arm substitution on the variability and levels of micronutrients B, Fe, Cu, Zn, Mn, and Ni in cottonseed from chromosome substitution (CS) cotton lines. Our hypothesis was that interspecific chromosome substitution in cotton can affect cottonseed micronutrients content, resulting in significant differences and variabilities of these nutrients among CS lines and between CS lines and the controls. Nine CS lines were grown in two-field experiments at two locations (in 2013 in South Carolina, USA; and in 2014 in Mississippi, USA). TM-1 (the recurrent parent of the CS line) and AM UA48 (cultivar) were used as control. The results showed significant variability among CS lines compared to the controls AM UA48 and TM-1. For example, in South Carolina (SC), B concentration in cottonseed ranged from 10.35 mg kg-1 in CS-M02 to 13.67 mg kg-1 in CS-T04. The concentration of Cu ranged from 4.81 mg kg-1 in CS-B08sh to 7.65 mg kg-1 in CS-T02, and CS-T02 was higher than both controls. The concentration of Fe ranged from 36.09 mg kg-1 to 56.69 mg kg-1 (an increase up to 57%), and six CS lines (CS-B02, CS-B08sh, CS-M02, CS-M04, CS-T02, and CS-T04) had higher concentration than both controls in 2013. In 2014 at the Mississippi location (MS), similar observation was found with CS lines for micronutrients content. The CS lines with higher concentrations of these micronutrients can be used as a genetic tool toward QTL identification for desired seed traits because these lines are genetically similar with TM-1, except the substituted chromosome or chromosome segment pairs from the alien species. Chromosome substitution provides an effective means for upland cotton improvement by targeted interspecific introgression, yielding CS lines that facilitate trait discovery, such as seed micronutritional qualities, due to increased isogenicity and markedly reduced complexity from epistatic interactions with non-target alien chromosomes. The positive correlation between B, Cu, and Fe at both locations, between Ni and Mn, between Zn and Cu, and between Zn and Ni at both locations signify the importance of a good agricultural and fertilizer management of these nutrients to maintain higher cottonseed nutrient content.
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Affiliation(s)
- Nacer Bellaloui
- Crop Genetics Research Unit, USDA, Agriculture Research Service, 141 Experiment Station Road, Stoneville, MS 38776, USA; (J.L.T.); (J.A.S.)
| | - Sukumar Saha
- Genetics and Sustainable Agriculture Research Unit, USDA, Agriculture Research Service, 810 Highway 12 East, Starkville, MS 39762, USA; (S.S.); (J.N.J.); (J.C.M.)
| | - Jennifer L. Tonos
- Crop Genetics Research Unit, USDA, Agriculture Research Service, 141 Experiment Station Road, Stoneville, MS 38776, USA; (J.L.T.); (J.A.S.)
| | - Jodi A. Scheffler
- Crop Genetics Research Unit, USDA, Agriculture Research Service, 141 Experiment Station Road, Stoneville, MS 38776, USA; (J.L.T.); (J.A.S.)
| | - Johnie N. Jenkins
- Genetics and Sustainable Agriculture Research Unit, USDA, Agriculture Research Service, 810 Highway 12 East, Starkville, MS 39762, USA; (S.S.); (J.N.J.); (J.C.M.)
| | - Jack C. McCarty
- Genetics and Sustainable Agriculture Research Unit, USDA, Agriculture Research Service, 810 Highway 12 East, Starkville, MS 39762, USA; (S.S.); (J.N.J.); (J.C.M.)
| | - David M. Stelly
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA;
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Zaidi SS, Naqvi RZ, Asif M, Strickler S, Shakir S, Shafiq M, Khan AM, Amin I, Mishra B, Mukhtar MS, Scheffler BE, Scheffler JA, Mueller LA, Mansoor S. Molecular insight into cotton leaf curl geminivirus disease resistance in cultivated cotton (Gossypium hirsutum). Plant Biotechnol J 2020; 18:691-706. [PMID: 31448544 PMCID: PMC7004920 DOI: 10.1111/pbi.13236] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/01/2019] [Accepted: 08/15/2019] [Indexed: 05/21/2023]
Abstract
Cultivated cotton (Gossypium hirsutum) is the most important fibre crop in the world. Cotton leaf curl disease (CLCuD) is the major limiting factor and a threat to textile industry in India and Pakistan. All the local cotton cultivars exhibit moderate to no resistance against CLCuD. In this study, we evaluated an exotic cotton accession Mac7 as a resistance source to CLCuD by challenging it with viruliferous whiteflies and performing qPCR to evaluate the presence/absence and relative titre of CLCuD-associated geminiviruses/betasatellites. The results indicated that replication of pathogenicity determinant betasatellite is significantly attenuated in Mac7 and probably responsible for resistance phenotype. Afterwards, to decipher the genetic basis of CLCuD resistance in Mac7, we performed RNA sequencing on CLCuD-infested Mac7 and validated RNA-Seq data with qPCR on 24 independent genes. We performed co-expression network and pathway analysis for regulation of geminivirus/betasatellite-interacting genes. We identified nine novel modules with 52 hubs of highly connected genes in network topology within the co-expression network. Analysis of these hubs indicated the differential regulation of auxin stimulus and cellular localization pathways in response to CLCuD. We also analysed the differential regulation of geminivirus/betasatellite-interacting genes in Mac7. We further performed the functional validation of selected candidate genes via virus-induced gene silencing (VIGS). Finally, we evaluated the genomic context of resistance responsive genes and found that these genes are not specific to A or D sub-genomes of G. hirsutum. These results have important implications in understanding CLCuD resistance mechanism and developing a durable resistance in cultivated cotton.
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Affiliation(s)
- Syed Shan‐e‐Ali Zaidi
- National Institute for Biotechnology and Genetic EngineeringFaisalabadPakistan
- Boyce Thompson InstituteIthacaNYUSA
- Plant Genetics LabTERRA Teaching and Research CenterGembloux Agro-Bio TechUniversity of LiègeGemblouxBelgium
| | - Rubab Zahra Naqvi
- National Institute for Biotechnology and Genetic EngineeringFaisalabadPakistan
- Boyce Thompson InstituteIthacaNYUSA
| | - Muhammad Asif
- National Institute for Biotechnology and Genetic EngineeringFaisalabadPakistan
| | | | - Sara Shakir
- National Institute for Biotechnology and Genetic EngineeringFaisalabadPakistan
- Boyce Thompson InstituteIthacaNYUSA
- Plant Genetics LabTERRA Teaching and Research CenterGembloux Agro-Bio TechUniversity of LiègeGemblouxBelgium
| | - Muhammad Shafiq
- National Institute for Biotechnology and Genetic EngineeringFaisalabadPakistan
- Present address:
Department of BiotechnologyUniversity of OkaraOkaraPakistan
| | - Abdul Manan Khan
- National Institute for Biotechnology and Genetic EngineeringFaisalabadPakistan
| | - Imran Amin
- National Institute for Biotechnology and Genetic EngineeringFaisalabadPakistan
| | - Bharat Mishra
- Department of BiologyUniversity of Alabama at BirminghamBirminghamALUSA
| | - M. Shahid Mukhtar
- Department of BiologyUniversity of Alabama at BirminghamBirminghamALUSA
| | - Brian E. Scheffler
- Genomics and Bioinformatics Research UnitUnited States Department of Agriculture‐Agricultural Research Service (USDA‐ARS)StonevilleMSUSA
| | - Jodi A. Scheffler
- Crop Genetics Research UnitUnited States Department of Agriculture‐Agricultural Research Service (USDA‐ARS)StonevilleMSUSA
| | | | - Shahid Mansoor
- National Institute for Biotechnology and Genetic EngineeringFaisalabadPakistan
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Hussain S, Farooq M, Malik HJ, Amin I, Scheffler BE, Scheffler JA, Liu SS, Mansoor S. Whole genome sequencing of Asia II 1 species of whitefly reveals that genes involved in virus transmission and insecticide resistance have genetic variances between Asia II 1 and MEAM1 species. BMC Genomics 2019; 20:507. [PMID: 31215403 PMCID: PMC6582559 DOI: 10.1186/s12864-019-5877-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 05/31/2019] [Indexed: 01/09/2023] Open
Abstract
Background Whiteflies (Bemisia tabaci) are phloem sap-sucking pests that because of their broad host range and ability to transmit viruses damage crop plants worldwide. B. tabaci are now known to be a complex of cryptic species that differ from each other in many characteristics such as mode of interaction with viruses, invasiveness, and resistance to insecticides. Asia II 1 is an indigenous species found on the Indian sub-continent and south-east Asia while the species named as Middle East Asia Minor 1 (MEAM1), likely originated from the Middle-East and has spread worldwide in recent decades. The purpose of this study is to find genomic differences between these two species. Results Sequencing of the nuclear genome of Asia II 1 with Illumina HiSeq and MiSeq generated 198.90 million reads that covers 88% of the reference genome. The sequence comparison with MEAM1 identified 2,327,972 SNPs and 202,479 INDELs. In Total, 1294 genes were detected with high impact variants. The functional analysis revealed that some of the genes are involved in virus transmission including 4 genes in Tomato yellow leaf curl virus (TYLCV) transmission, 96 in Tomato crinivirus (ToCV) transmission, and 14 genes in insecticide resistance. Conclusions These genetic differences between Asia II 1 and MEAM1 may underlie the major biological differences between the two species such as virus transmission, insecticide resistance, and range of host plants. The present study provides new genomic data and information resources for Asia II 1 that will not only contribute to the species delimitation of whitefly, but also help in conceiving future research studies to develop more targeted management strategies against whitefly. Electronic supplementary material The online version of this article (10.1186/s12864-019-5877-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sonia Hussain
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.,Department of Biotechnology, Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Muhammad Farooq
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Hassan Jamil Malik
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.,Department of Biotechnology, Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Imran Amin
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Brian E Scheffler
- USDA-ARS, Genomics and Bioinformatics Research Unit, 141 Experiment Station Rd., Stoneville, MS, 38776, USA
| | - Jodi A Scheffler
- USDA-ARS, Crop Genetics Research Unit, 141 Experiment Station Rd, Stoneville, MS, 38776, USA
| | - Shu-Sheng Liu
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.
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8
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Janga MR, Pandeya D, Campbell LM, Konganti K, Villafuerte ST, Puckhaber L, Pepper A, Stipanovic RD, Scheffler JA, Rathore KS. Genes regulating gland development in the cotton plant. Plant Biotechnol J 2019; 17:1142-1153. [PMID: 30467959 PMCID: PMC6523598 DOI: 10.1111/pbi.13044] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 11/12/2018] [Accepted: 11/20/2018] [Indexed: 05/21/2023]
Abstract
In seeds and other parts of cultivated, tetraploid cotton (Gossypium hirsutum L.), multicellular groups of cells lysigenously form dark glands containing toxic terpenoids such as gossypol that defend the plant against pests and pathogens. Using RNA-seq analysis of embryos from near-isogenic glanded (Gl2 Gl2 Gl3 Gl3 ) versus glandless (gl2 gl2 gl3 gl3 ) plants, we identified 33 genes that expressed exclusively or at higher levels in embryos just prior to gland formation in glanded plants. Virus-induced gene silencing against three gene pairs led to significant reductions in the number of glands in the leaves, and significantly lower levels of gossypol and related terpenoids. These genes encode transcription factors and have been designated the 'Cotton Gland Formation' (CGF) genes. No sequence differences were found between glanded and glandless cotton for CGF1 and CGF2 gene pairs. The glandless cotton has a transposon insertion within the coding sequence of the GoPGF (synonym CGF3) gene of the A subgenome and extensive mutations in the promoter of D subgenome homeolog. Overexpression of GoPGF (synonym CGF3) led to a dramatic increase in gossypol and related terpenoids in cultured cells, whereas CRISPR/Cas9 knockout of GoPGF (synonym CGF3) genes resulted in glandless phenotype. Taken collectively, the results show that the GoPGF (synonym CGF3) gene plays a critical role in the formation of glands in the cotton plant. Seed-specific silencing of CGF genes, either individually or in combination, could eliminate glands, thus gossypol, from the cottonseed to render it safe as food or feed for monogastrics.
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Affiliation(s)
- Madhusudhana R. Janga
- Institute for Plant Genomics and BiotechnologyTexas A&M UniversityCollege StationTXUSA
| | - Devendra Pandeya
- Institute for Plant Genomics and BiotechnologyTexas A&M UniversityCollege StationTXUSA
| | - LeAnne M. Campbell
- Institute for Plant Genomics and BiotechnologyTexas A&M UniversityCollege StationTXUSA
| | - Kranti Konganti
- Texas A&M Institute for Genome Sciences and SocietyTexas A&M UniversityCollege StationTXUSA
| | | | - Lorraine Puckhaber
- Southern Plains Agricultural Research CenterUSDA‐ARSCollege StationTXUSA
| | - Alan Pepper
- Department of BiologyTexas A&M UniversityCollege StationTXUSA
| | | | | | - Keerti S. Rathore
- Institute for Plant Genomics and BiotechnologyTexas A&M UniversityCollege StationTXUSA
- Department of Soil and Crop SciencesTexas A&M UniversityCollege StationTXUSA
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9
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Grover CE, Arick MA, Thrash A, Conover JL, Sanders WS, Peterson DG, Frelichowski JE, Scheffler JA, Scheffler BE, Wendel JF. Insights into the Evolution of the New World Diploid Cottons (Gossypium, Subgenus Houzingenia) Based on Genome Sequencing. Genome Biol Evol 2019; 11:53-71. [PMID: 30476109 PMCID: PMC6320677 DOI: 10.1093/gbe/evy256] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2018] [Indexed: 12/24/2022] Open
Abstract
We employed phylogenomic methods to study molecular evolutionary processes and phylogeny in the geographically widely dispersed New World diploid cottons (Gossypium, subg. Houzingenia). Whole genome resequencing data (average of 33× genomic coverage) were generated to reassess the phylogenetic history of the subgenus and provide a temporal framework for its diversification. Phylogenetic analyses indicate that the subgenus likely originated following transoceanic dispersal from Africa about 6.6 Ma, but that nearly all of the biodiversity evolved following rapid diversification in the mid-Pleistocene (0.5-2.0 Ma), with multiple long-distance dispersals required to account for range expansion to Arizona, the Galapagos Islands, and Peru. Comparative analyses of cpDNAversus nuclear data indicate that this history was accompanied by several clear cases of interspecific introgression. Repetitive DNAs contribute roughly half of the total 880 Mb genome, but most transposable element families are relatively old and stable among species. In the genic fraction, pairwise synonymous mutation rates average 1% per Myr, with nonsynonymous changes being about seven times less frequent. Over 1.1 million indels were detected and phylogenetically polarized, revealing a 2-fold bias toward deletions over small insertions. We suggest that this genome down-sizing bias counteracts genome size growth by TE amplification and insertions, and helps explain the relatively small genomes that are restricted to this subgenus. Compared with the rate of nucleotide substitution, the rate of indel occurrence is much lower averaging about 17 nucleotide substitutions per indel event.
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Affiliation(s)
- Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University
| | - Mark A Arick
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University
| | - Adam Thrash
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University
| | - Justin L Conover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University
| | - William S Sanders
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University
- Department of Computer Science & Engineering, Mississippi State University
- The Jackson Laboratory, Connecticut
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University
| | | | | | - Brian E Scheffler
- USDA, Genomics and Bioinformatics Research Unit, Stoneville, Mississippi
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University
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10
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Naqvi RZ, Zaidi SSEA, Akhtar KP, Strickler S, Woldemariam M, Mishra B, Mukhtar MS, Scheffler BE, Scheffler JA, Jander G, Mueller LA, Asif M, Mansoor S. Transcriptomics reveals multiple resistance mechanisms against cotton leaf curl disease in a naturally immune cotton species, Gossypium arboreum. Sci Rep 2017; 7:15880. [PMID: 29162860 PMCID: PMC5698292 DOI: 10.1038/s41598-017-15963-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/03/2017] [Indexed: 12/13/2022] Open
Abstract
Cotton leaf curl disease (CLCuD), caused by cotton leaf curl viruses (CLCuVs), is among the most devastating diseases in cotton. While the widely cultivated cotton species Gossypium hirsutum is generally susceptible, the diploid species G. arboreum is a natural source for resistance against CLCuD. However, the influence of CLCuD on the G. arboreum transcriptome and the interaction of CLCuD with G. arboreum remains to be elucidated. Here we have used an RNA-Seq based study to analyze differential gene expression in G. arboreum under CLCuD infestation. G. arboreum plants were infested by graft inoculation using a CLCuD infected scion of G. hirsutum. CLCuD infested asymptomatic and symptomatic plants were analyzed with RNA-seq using an Illumina HiSeq. 2500. Data analysis revealed 1062 differentially expressed genes (DEGs) in G. arboreum. We selected 17 genes for qPCR to validate RNA-Seq data. We identified several genes involved in disease resistance and pathogen defense. Furthermore, a weighted gene co-expression network was constructed from the RNA-Seq dataset that indicated 50 hub genes, most of which are involved in transport processes and might have a role in the defense response of G. arboreum against CLCuD. This fundamental study will improve the understanding of virus-host interaction and identification of important genes involved in G. arboreum tolerance against CLCuD.
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Affiliation(s)
- Rubab Zahra Naqvi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Punjab, Pakistan
- Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
- Boyce Thompson Institute, 533 Tower Road, Cornell University, Ithaca, NY, USA
| | - Syed Shan-E-Ali Zaidi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Punjab, Pakistan
- Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
- Boyce Thompson Institute, 533 Tower Road, Cornell University, Ithaca, NY, USA
- AgroBioChem Department, Gembloux Agro-Bio Tech, University of Liège, 5030, Gembloux, Belgium
| | - Khalid Pervaiz Akhtar
- Nuclear Institute for Agriculture & Biology (NIAB), Jhang Road, Faisalabad, Punjab, Pakistan
| | - Susan Strickler
- Boyce Thompson Institute, 533 Tower Road, Cornell University, Ithaca, NY, USA
| | - Melkamu Woldemariam
- Boyce Thompson Institute, 533 Tower Road, Cornell University, Ithaca, NY, USA
| | - Bharat Mishra
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - M Shahid Mukhtar
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Brian E Scheffler
- Genomics and Bioinformatics Research Unit (USDA-ARS), Stoneville, MS, USA
| | - Jodi A Scheffler
- Crop Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Stoneville, MS, USA
| | - Georg Jander
- Boyce Thompson Institute, 533 Tower Road, Cornell University, Ithaca, NY, USA
| | - Lukas A Mueller
- Boyce Thompson Institute, 533 Tower Road, Cornell University, Ithaca, NY, USA
| | - Muhammad Asif
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Punjab, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Punjab, Pakistan.
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11
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Saski CA, Scheffler BE, Hulse-Kemp AM, Liu B, Song Q, Ando A, Stelly DM, Scheffler JA, Grimwood J, Jones DC, Peterson DG, Schmutz J, Chen ZJ. Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids. Sci Rep 2017; 7:15274. [PMID: 29127298 PMCID: PMC5681701 DOI: 10.1038/s41598-017-14885-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 10/18/2017] [Indexed: 01/06/2023] Open
Abstract
Like those of many agricultural crops, the cultivated cotton is an allotetraploid and has a large genome (~2.5 gigabase pairs). The two sub genomes, A and D, are highly similar but unequally sized and repeat-rich, which pose significant challenges for accurate genome reconstruction using standard approaches. Here we report the development of BAC libraries, sub genome specific physical maps, and a new-generation sequencing approach that will lead to a reference-grade genome assembly for Upland cotton. Three BAC libraries were constructed, fingerprinted, and integrated with BAC-end sequences (BES) to produce a de novo whole-genome physical map. The BAC map was partitioned by sub genomes through alignment to the diploid progenitor D-genome reference sequence with densely spaced BES anchor points and computational filtering. The physical maps were validated with FISH and genetic mapping of SNP markers derived from BES. Two pairs of homeologous chromosomes, A11/D11 and A12/D12, were used to assess multiplex sequencing approaches for completeness and scalability. The results represent the first sub genome anchored physical maps of Upland cotton, and a new-generation approach to the whole-genome sequencing, which will lead to the reference-grade assembly of allopolyploid cotton and serve as a general strategy for sequencing other polyploid species.
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Affiliation(s)
| | - Brian E Scheffler
- USDA-ARS, Genomics and Bioinformatics Research Unit, Stoneville, MS, USA
| | - Amanda M Hulse-Kemp
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
| | - Bo Liu
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
| | - Qingxin Song
- Department of Molecular Biosciences, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, University of Texas, Austin, TX, 78712, USA
| | - Atsumi Ando
- Department of Molecular Biosciences, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, University of Texas, Austin, TX, 78712, USA
| | - David M Stelly
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
| | | | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Don C Jones
- Agriculture and Environmental Research, Cotton Incorporated, Cary, NC, USA
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing & Biotechnology and Department of Plant & Soil Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
| | - Z Jeffery Chen
- Department of Molecular Biosciences, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, University of Texas, Austin, TX, 78712, USA.
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12
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Zubair M, Zaidi SSEA, Shakir S, Farooq M, Amin I, Scheffler JA, Scheffler BE, Mansoor S. Multiple begomoviruses found associated with cotton leaf curl disease in Pakistan in early 1990 are back in cultivated cotton. Sci Rep 2017; 7:680. [PMID: 28386113 PMCID: PMC5429635 DOI: 10.1038/s41598-017-00727-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 03/10/2017] [Indexed: 11/09/2022] Open
Abstract
The first epidemic of cotton leaf curl disease (CLCuD) in early 1990's in the Indian subcontinent was associated with several distinct begomoviruses along with a disease-specific betasatellite. Resistant cotton varieties were introduced in late 1990's but soon resistance was broken and was associated with a single recombinant begomovirus named Burewala strain of Cotton leaf curl Kokhran virus that lacks a full complement of a gene encoding a transcription activator protein (TrAP). In order to understand the ongoing changes in CLCuD complex in Pakistan, CLCuD affected plants from cotton fields at Vehari were collected. Illumina sequencing was used to assess the diversity of CLCuD complex. At least three distinct begomoviruses characterized from the first epidemic; Cotton leaf curl Multan virus, Cotton leaf curl Kokhran virus and Cotton leaf curl Alabad virus, several distinct species of alphasatellites and cotton leaf curl Multan betasatellite were found associated with CLCuD. These viruses were also cloned and sequenced through Sanger sequencing to confirm the identity of the begomoviruses and that all clones possessed a full complement of the TrAP gene. A new strain of betasatellite was identified here and named CLCuMuBVeh. The implications of these findings in efforts to control CLCuD are discussed.
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Affiliation(s)
- Muhammad Zubair
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Syed Shan-E-Ali Zaidi
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Sara Shakir
- Centre for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Farooq
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Imran Amin
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Jodi A Scheffler
- USDA-ARS, Crop Genetics Research Unit, 141 Experiment Station Rd, Stoneville, MS, 38776, USA
| | - Brian E Scheffler
- USDA-ARS, Genomics and Bioinformatics Research Unit, 141 Experiment Station Rd, Stoneville, MS, 38776, USA
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.
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13
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Hinze LL, Hulse-Kemp AM, Wilson IW, Zhu QH, Llewellyn DJ, Taylor JM, Spriggs A, Fang DD, Ulloa M, Burke JJ, Giband M, Lacape JM, Van Deynze A, Udall JA, Scheffler JA, Hague S, Wendel JF, Pepper AE, Frelichowski J, Lawley CT, Jones DC, Percy RG, Stelly DM. Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array. BMC Plant Biol 2017; 17:37. [PMID: 28158969 PMCID: PMC5291959 DOI: 10.1186/s12870-017-0981-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 01/23/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Cotton germplasm resources contain beneficial alleles that can be exploited to develop germplasm adapted to emerging environmental and climate conditions. Accessions and lines have traditionally been characterized based on phenotypes, but phenotypic profiles are limited by the cost, time, and space required to make visual observations and measurements. With advances in molecular genetic methods, genotypic profiles are increasingly able to identify differences among accessions due to the larger number of genetic markers that can be measured. A combination of both methods would greatly enhance our ability to characterize germplasm resources. Recent efforts have culminated in the identification of sufficient SNP markers to establish high-throughput genotyping systems, such as the CottonSNP63K array, which enables a researcher to efficiently analyze large numbers of SNP markers and obtain highly repeatable results. In the current investigation, we have utilized the SNP array for analyzing genetic diversity primarily among cotton cultivars, making comparisons to SSR-based phylogenetic analyses, and identifying loci associated with seed nutritional traits. RESULTS The SNP markers distinctly separated G. hirsutum from other Gossypium species and distinguished the wild from cultivated types of G. hirsutum. The markers also efficiently discerned differences among cultivars, which was the primary goal when designing the CottonSNP63K array. Population structure within the genus compared favorably with previous results obtained using SSR markers, and an association study identified loci linked to factors that affect cottonseed protein content. CONCLUSIONS Our results provide a large genome-wide variation data set for primarily cultivated cotton. Thousands of SNPs in representative cotton genotypes provide an opportunity to finely discriminate among cultivated cotton from around the world. The SNPs will be relevant as dense markers of genome variation for association mapping approaches aimed at correlating molecular polymorphisms with variation in phenotypic traits, as well as for molecular breeding approaches in cotton.
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Affiliation(s)
- Lori L. Hinze
- USDA-ARS, Crop Germplasm Research Unit, College Station, TX 77845 USA
| | - Amanda M. Hulse-Kemp
- Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, CA 95616 USA
| | - Iain W. Wilson
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Qian-Hao Zhu
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Danny J. Llewellyn
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Jen M. Taylor
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Andrew Spriggs
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - David D. Fang
- USDA-ARS, Cotton Fiber Bioscience Research Unit, New Orleans, LA 70124 USA
| | - Mauricio Ulloa
- USDA-ARS, Cropping Systems Research Laboratory, Plant Stress and Germplasm Development Research Unit, Lubbock, TX 79415 USA
| | - John J. Burke
- USDA-ARS, Cropping Systems Research Laboratory, Plant Stress and Germplasm Development Research Unit, Lubbock, TX 79415 USA
| | - Marc Giband
- CIRAD, UMR AGAP, Montpellier, F34398 France
- EMBRAPA, Algodão, Nucleo Cerrado, 75.375-000 Santo Antônio de Goias, GO Brazil
| | | | - Allen Van Deynze
- Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, CA 95616 USA
| | - Joshua A. Udall
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602 USA
| | - Jodi A. Scheffler
- USDA-ARS, Jamie Whitten Delta States Research Center, Stoneville, MS 38776 USA
| | - Steve Hague
- Department of Soil & Crop Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011 USA
| | - Alan E. Pepper
- Department of Biology, Texas A&M University, College Station, TX 77843 USA
- Interdisciplinary Department of Genetics, Texas A&M University, College Station, TX 77843 USA
| | | | - Cindy T. Lawley
- Illumina Inc., 499 Illinois Street, San Francisco, CA 94158 USA
| | - Don C. Jones
- Cotton Incorporated, Agricultural Research, Cary, NC 27513 USA
| | - Richard G. Percy
- USDA-ARS, Crop Germplasm Research Unit, College Station, TX 77845 USA
| | - David M. Stelly
- Department of Soil & Crop Sciences, Texas A&M University, College Station, TX 77843 USA
- Interdisciplinary Department of Genetics, Texas A&M University, College Station, TX 77843 USA
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14
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Malik HJ, Raza A, Amin I, Scheffler JA, Scheffler BE, Brown JK, Mansoor S. RNAi-mediated mortality of the whitefly through transgenic expression of double-stranded RNA homologous to acetylcholinesterase and ecdysone receptor in tobacco plants. Sci Rep 2016; 6:38469. [PMID: 27929123 PMCID: PMC5143975 DOI: 10.1038/srep38469] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 11/10/2016] [Indexed: 01/09/2023] Open
Abstract
The whitefly Bemisia tabaci (Genn.) is a pest and vector of plant viruses to crop and ornamental plants worldwide. Using RNA interference (RNAi) to down regulate whitefly genes by expressing their homologous double stranded RNAs in plants has great potential for management of whiteflies to reduce plant virus disease spread. Using a Tobacco rattle virus-derived plasmid for in planta transient expression of double stranded RNA (dsRNA) homologous to the acetylcholinesterase (AChE) and ecdysone receptor (EcR) genes of B. tabaci, resulted in significant adult whitefly mortality. Nicotiana tabacum L. plants expressing dsRNA homologous to B. tabaci AChE and EcR were constructed by fusing sequences derived from both genes. Mortality of adult whiteflies exposed to dsRNA by feeding on N. tabacum plants, compared to non-dsRNA expressing plants, recorded at 24-hr intervals post-ingestion for three days, was >90% and 10%, respectively. Analysis of gene expression by real time quantitative PCR indicated that whitefly mortality was attributable to the down-regulation of both target genes by RNAi. Results indicated that knock down of whitefly genes involved in neuronal transmission and transcriptional activation of developmental genes, has potential as a bio-pesticide to reduce whitefly population size and thereby decrease virus spread.
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Affiliation(s)
- Hassan Jamil Malik
- Molecular Virology and Gene Silencing Laboratory, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, PO Box #577, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Amir Raza
- Molecular Virology and Gene Silencing Laboratory, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, PO Box #577, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Imran Amin
- Molecular Virology and Gene Silencing Laboratory, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, PO Box #577, Faisalabad, Pakistan
| | - Jodi A. Scheffler
- USDA-ARS, Crop Genetics Research Unit, 141 Experiment Station Rd, Stoneville, MS 38776, USA
| | - Brian E. Scheffler
- USDA-ARS, Genomics and Bioinformatics Research Unit, 141 Experiment Station Rd, Stoneville, MS 38776, USA
| | - Judith K. Brown
- School of Plant Sciences, The University of Arizona, Tucson, AZ 85721, USA
| | - Shahid Mansoor
- Molecular Virology and Gene Silencing Laboratory, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, PO Box #577, Faisalabad, Pakistan
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15
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Zaidi SSEA, Shafiq M, Amin I, Scheffler BE, Scheffler JA, Briddon RW, Mansoor S. Frequent Occurrence of Tomato Leaf Curl New Delhi Virus in Cotton Leaf Curl Disease Affected Cotton in Pakistan. PLoS One 2016; 11:e0155520. [PMID: 27213535 PMCID: PMC4877078 DOI: 10.1371/journal.pone.0155520] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 04/29/2016] [Indexed: 11/18/2022] Open
Abstract
Cotton leaf curl disease (CLCuD) is the major biotic constraint to cotton production on the Indian subcontinent, and is caused by monopartite begomoviruses accompanied by a specific DNA satellite, Cotton leaf curl Multan betasatellite (CLCuMB). Since the breakdown of resistance against CLCuD in 2001/2002, only one virus, the "Burewala" strain of Cotton leaf curl Kokhran virus (CLCuKoV-Bur), and a recombinant form of CLCuMB have consistently been identified in cotton across the major cotton growing areas of Pakistan. Unusually a bipartite isolate of the begomovirus Tomato leaf curl virus was identified in CLCuD-affected cotton recently. In the study described here we isolated the bipartite begomovirus Tomato leaf curl New Delhi virus (ToLCNDV) from CLCuD-affected cotton. To assess the frequency and geographic occurrence of ToLCNDV in cotton, CLCuD-symptomatic cotton plants were collected from across the Punjab and Sindh provinces between 2013 and 2015. Analysis of the plants by diagnostic PCR showed the presence of CLCuKoV-Bur in all 31 plants examined and ToLCNDV in 20 of the samples. Additionally, a quantitative real-time PCR analysis of the levels of the two viruses in co-infected plants suggests that coinfection of ToLCNDV with the CLCuKoV-Bur/CLCuMB complex leads to an increase in the levels of CLCuMB, which encodes the major pathogenicity (symptom) determinant of the complex. The significance of these results are discussed.
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Affiliation(s)
- Syed Shan-E-Ali Zaidi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, P O Box 577, Jhang Road, Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Muhammad Shafiq
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, P O Box 577, Jhang Road, Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, P O Box 577, Jhang Road, Faisalabad, Pakistan
| | - Brian E Scheffler
- Genomics and Bioinformatics Research Unit, 141 Experiment Station Rd., Stoneville, Mississippi, 38776, United States of America
| | - Jodi A Scheffler
- Crop Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Stoneville, Mississippi, United States of America
| | - Rob W Briddon
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, P O Box 577, Jhang Road, Faisalabad, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, P O Box 577, Jhang Road, Faisalabad, Pakistan
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16
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Raza A, Malik HJ, Shafiq M, Amin I, Scheffler JA, Scheffler BE, Mansoor S. RNA Interference based Approach to Down Regulate Osmoregulators of Whitefly (Bemisia tabaci): Potential Technology for the Control of Whitefly. PLoS One 2016; 11:e0153883. [PMID: 27105353 PMCID: PMC4841547 DOI: 10.1371/journal.pone.0153883] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Accepted: 04/05/2016] [Indexed: 01/09/2023] Open
Abstract
Over the past decade RNA interference (RNAi) technology has emerged as a successful tool not only for functional genomics, but in planta expression of short interfering RNAs (siRNAs) that could offer great potential for insect pest management. The diet of insects feeding exclusively on phloem sieves contains water and sugars as main components, and the uptake of the liquid food greatly depends on the osmotic pressure within the insect body. Based on this physiological mechanism, transgenic plants of Nicotiana tabacum were generated expressing double stranded RNA (dsRNA) against both aquaporin (AQP) and a sucrase gene, alpha glucosidase (AGLU). These two genes are involved in osmotic pressure maintenance particularly in sap sucking insects, and the aim was to disrupt osmoregulation within the insect ultimately leading to mortality. Real time quantitative PCR (RT-qPCR) was performed to assess the suppression of gene expression in Bemisia tabaci (B. tabaci) and mortality was recorded during transgenic tobacco feeding bioassays. Feeding of insects on plants expressing dsRNA significantly reduced the transcript level of the target genes in B. tabaci after six days of feeding and more than 70% mortality was observed in B. tabaci fed on transgenic plants compared to the control plants. Our data shows that down-regulation of genes related to osmoregulation may find practical applications for the control of this important pest in cotton and other crops.
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Affiliation(s)
- Amir Raza
- Molecular Virology and Gene Silencing Laboratory, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, PO Box # 577, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Hassan Jamil Malik
- Molecular Virology and Gene Silencing Laboratory, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, PO Box # 577, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Muhammad Shafiq
- Molecular Virology and Gene Silencing Laboratory, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, PO Box # 577, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Imran Amin
- Molecular Virology and Gene Silencing Laboratory, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, PO Box # 577, Faisalabad, Pakistan
| | - Jodi A. Scheffler
- USDA-ARS, Crop Genetics Research Unit, 141 Experiment Station Rd, Stoneville, Mississippi, 38776, United States of America
| | - Brian E. Scheffler
- USDA-ARS, Genomics and Bioinformatics Research Unit, 141 Experiment Station Rd, Stoneville, Mississippi, 38776, United States of America
| | - Shahid Mansoor
- Molecular Virology and Gene Silencing Laboratory, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, PO Box # 577, Faisalabad, Pakistan
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Hulse-Kemp AM, Lemm J, Plieske J, Ashrafi H, Buyyarapu R, Fang DD, Frelichowski J, Giband M, Hague S, Hinze LL, Kochan KJ, Riggs PK, Scheffler JA, Udall JA, Ulloa M, Wang SS, Zhu QH, Bag SK, Bhardwaj A, Burke JJ, Byers RL, Claverie M, Gore MA, Harker DB, Islam MS, Jenkins JN, Jones DC, Lacape JM, Llewellyn DJ, Percy RG, Pepper AE, Poland JA, Mohan Rai K, Sawant SV, Singh SK, Spriggs A, Taylor JM, Wang F, Yourstone SM, Zheng X, Lawley CT, Ganal MW, Van Deynze A, Wilson IW, Stelly DM. Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp. G3 (Bethesda) 2015; 5:1187-209. [PMID: 25908569 PMCID: PMC4478548 DOI: 10.1534/g3.115.018416] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 04/11/2015] [Indexed: 11/18/2022]
Abstract
High-throughput genotyping arrays provide a standardized resource for plant breeding communities that are useful for a breadth of applications including high-density genetic mapping, genome-wide association studies (GWAS), genomic selection (GS), complex trait dissection, and studying patterns of genomic diversity among cultivars and wild accessions. We have developed the CottonSNP63K, an Illumina Infinium array containing assays for 45,104 putative intraspecific single nucleotide polymorphism (SNP) markers for use within the cultivated cotton species Gossypium hirsutum L. and 17,954 putative interspecific SNP markers for use with crosses of other cotton species with G. hirsutum. The SNPs on the array were developed from 13 different discovery sets that represent a diverse range of G. hirsutum germplasm and five other species: G. barbadense L., G. tomentosum Nuttal × Seemann, G. mustelinum Miers × Watt, G. armourianum Kearny, and G. longicalyx J.B. Hutchinson and Lee. The array was validated with 1,156 samples to generate cluster positions to facilitate automated analysis of 38,822 polymorphic markers. Two high-density genetic maps containing a total of 22,829 SNPs were generated for two F2 mapping populations, one intraspecific and one interspecific, and 3,533 SNP markers were co-occurring in both maps. The produced intraspecific genetic map is the first saturated map that associates into 26 linkage groups corresponding to the number of cotton chromosomes for a cross between two G. hirsutum lines. The linkage maps were shown to have high levels of collinearity to the JGI G. raimondii Ulbrich reference genome sequence. The CottonSNP63K array, cluster file and associated marker sequences constitute a major new resource for the global cotton research community.
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Affiliation(s)
- Amanda M Hulse-Kemp
- Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843 Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843
| | - Jana Lemm
- TraitGenetics GmbH, 06466 Gatersleben, Germany
| | | | - Hamid Ashrafi
- Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, California 95616
| | - Ramesh Buyyarapu
- Dow AgroSciences, Trait Genetics and Technologies, Indianapolis, Indiana 46268
| | - David D Fang
- USDA-ARS-SRRC, Cotton Fiber Bioscience Research Unit, New Orleans, Louisiana 70124
| | - James Frelichowski
- USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845
| | - Marc Giband
- CIRAD, UMR AGAP, Montpellier, F34398, France EMBRAPA, Algodão, Nucleo Cerrado, 75.375-000 Santo Antônio de Goias, GO, Brazil
| | - Steve Hague
- Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843
| | - Lori L Hinze
- USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845
| | - Kelli J Kochan
- Department of Animal Science, Texas A&M University, College Station, Texas 77843
| | - Penny K Riggs
- Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843 Department of Animal Science, Texas A&M University, College Station, Texas 77843
| | - Jodi A Scheffler
- USDA-ARS, Jamie Whitten Delta States Research Center, Stoneville, Mississippi 38776
| | - Joshua A Udall
- Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602
| | - Mauricio Ulloa
- USDA-ARS, PA, Plant Stress and Germplasm Development Research Unit, Lubbock, Texas 79415
| | - Shirley S Wang
- USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845
| | - Qian-Hao Zhu
- CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia
| | - Sumit K Bag
- CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India
| | - Archana Bhardwaj
- CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India
| | - John J Burke
- USDA-ARS, PA, Plant Stress and Germplasm Development Research Unit, Lubbock, Texas 79415
| | - Robert L Byers
- Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602
| | | | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
| | - David B Harker
- Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602
| | - Md S Islam
- USDA-ARS-SRRC, Cotton Fiber Bioscience Research Unit, New Orleans, Louisiana 70124
| | - Johnie N Jenkins
- USDA-ARS, Genetics and Precision Agriculture Research, Mississippi State, Mississippi 39762
| | - Don C Jones
- Cotton Incorporated, Agricultural Research, Cary, North Carolina 27513
| | | | - Danny J Llewellyn
- CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia
| | - Richard G Percy
- USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845
| | - Alan E Pepper
- Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843 Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Jesse A Poland
- Wheat Genetics Resource Center, Department of Plant Pathology and Department of Agronomy, Kansas State University, Manhattan, Kansas 66506
| | - Krishan Mohan Rai
- CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India
| | - Samir V Sawant
- CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India
| | - Sunil Kumar Singh
- CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India
| | - Andrew Spriggs
- CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia
| | - Jen M Taylor
- CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia
| | - Fei Wang
- Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843
| | - Scott M Yourstone
- Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602
| | - Xiuting Zheng
- Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843
| | | | | | - Allen Van Deynze
- Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, California 95616
| | - Iain W Wilson
- CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia
| | - David M Stelly
- Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843 Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843
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Scheffler JA, Romano GB, Blanco CA. Evaluating host plant resistance in cotton (<i>Gossypium hirsutum</i> L.) with varying gland densities to tobacco budworm (<i>Heliothis virescens</i> F.) and bollworm (<i>Helicoverpa zea</i> Boddie) in the field and laboratory. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/as.2012.31004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Romano GB, Sacks EJ, Stetina SR, Robinson AF, Fang DD, Gutierrez OA, Scheffler JA. Identification and genomic location of a reniform nematode (Rotylenchulus reniformis) resistance locus (Ren ari) introgressed from Gossypium aridum into upland cotton (G. hirsutum). Theor Appl Genet 2009; 120:139-50. [PMID: 19830404 PMCID: PMC2778618 DOI: 10.1007/s00122-009-1165-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Accepted: 09/27/2009] [Indexed: 05/25/2023]
Abstract
In this association mapping study, a tri-species hybrid, [Gossypium arboreum x (G. hirsutum x G. aridum)(2)], was crossed with MD51ne (G. hirsutum) and progeny from the cross were used to identify and map SSR markers associated with reniform nematode (Rotylenchulus reniformis) resistance. Seventy-six progeny (the 50 most resistant and 26 most susceptible) plants were genotyped with 104 markers. Twenty-five markers were associated with a resistance locus that we designated Ren(ari) and two markers, BNL3279_132 and BNL2662_090, mapped within 1 cM of Ren(ari). Because the SSR fragments associated with resistance were found in G. aridum and the bridging line G 371, G. aridum is the likely source of this resistance. The resistance is simply inherited, possibly controlled by a single dominant gene. The markers identified in this project are a valuable resource to breeders and geneticists in the quest to produce cotton cultivars with a high level of resistance to reniform nematode.
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Affiliation(s)
| | - Erik J. Sacks
- USDA/ARS, 141 Experiment Station Rd, Stoneville, MS 38776 USA
- Present Address: Mendel Biotechnology, 3935 Point Eden Way, Hayward, CA 94545 USA
| | | | | | - David D. Fang
- USDA/ARS, 141 Experiment Station Rd, Stoneville, MS 38776 USA
| | - Osman A. Gutierrez
- Department of Plant and Soil Sciences, Mississippi State University, P. O. Box 5367, Mississippi State, MS 39762 USA
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Arias RS, Stetina SR, Tonos JL, Scheffler JA, Scheffler BE. Microsatellites reveal genetic diversity in Rotylenchulus reniformis populations. J Nematol 2009; 41:146-56. [PMID: 22661788 PMCID: PMC3365315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2009] [Indexed: 06/01/2023] Open
Abstract
Rotylenchulus reniformis is the predominant parasitic nematode of cotton in the Mid South area of the United States. Although variable levels of infection and morphological differences have been reported for this nematode, genetic variability has been more elusive. We developed microsatellite-enriched libraries for R. reniformis, produced 1152 clones, assembled 694 contigs, detected 783 simple sequence repeats (SSR) and designed 192 SSR-markers. The markers were tested on six R. reniformis cultures from four states, Texas, Louisiana, Mississippi and Georgia, in the USA. Based on performance we selected 156 SSR markers for R. reniformis from which 88 were polymorphic across the six reniform nematode populations, showing as the most frequent motif the dinucleotide AG. The polymorphic information content of the markers ranged from 0.00 to 0.82, and the percentage of multiallelic loci of the isolates was between 40.9 and 45.1%. An interesting finding in this study was the genetic variability detected among the three Mississippi isolates, for which 22 SSR markers were polymorphic. We also tested the level of infection of these isolates on six cotton genotypes, where significant differences were found between the Texas and Georgia isolates. Coincidentally, 62 polymorphic markers were able to distinguish these two populations. Further studies will be necessary to establish possible connections, if any, between markers and level of pathogenicity of the nematode. The SSR markers developed here will be useful in the assessment of the genetic diversity of this nematode, could assist in management practices for control of reniform nematode, be used in breeding programs for crop resistance, and help in detecting the origin and spread of this nematode in the United States.
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Affiliation(s)
- Renée S Arias
- USDA-ARS MSA Genomics and Bioinformatics Research Unit, 141 Experiment Station Rd., Stoneville, MS 38776, USA USDA-ARS MSA Crop Genetics and Production Research Unit, 141 Experiment Station Rd. Stoneville, MS 38776, USA
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Scheffler JA, Parkinson R, Dale PJ. Frequency and distance of pollen dispersal from transgenic oilseed rape (Brassica napus). Transgenic Res 1993. [DOI: 10.1007/bf01976177] [Citation(s) in RCA: 87] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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