1
|
Adhikari J, Chandnani R, Vitrakoti D, Khanal S, Ployaram W, Paterson AH. Comparative transmission genetics of introgressed chromatin in reciprocal advanced backcross populations in Gossypium (cotton) polyploids. Heredity (Edinb) 2023; 130:209-222. [PMID: 36754975 PMCID: PMC10076365 DOI: 10.1038/s41437-023-00594-w] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 01/11/2023] [Accepted: 01/23/2023] [Indexed: 02/10/2023] Open
Abstract
Introgression is a potential source of valuable genetic variation and interspecific introgression lines are important resources for plant breeders to access novel alleles. Experimental advanced-generation backcross populations contain individuals with genomic compositions similar to those resulting from natural interspecific hybridization and provide opportunities to study the nature and transmission pattern of donor chromatin in recipient genomes. Here, we analyze transmission of donor chromatin in reciprocal backcrosses between G. hirsutum and G. barbadense. Across the genome, recurrent backcrossing in both backgrounds yielded donor chromatin at slightly higher frequencies than the Mendelian expectation in BC5F1 plants, while the average frequency of donor alleles in BC5F2 segregating families was less than expected. In the two subgenomes of polyploid cotton, the rate of donor chromatin introgression was similar. Although donor chromatin was tolerated over much of the recipient genomes, 21 regions recalcitrant to donor alleles were identified. Only limited correspondence is observed between the recalcitrant regions in the two backgrounds, suggesting the effect of species background on introgression of donor segments. Genetic breakdown was progressive, with floral abscission and seed inviability ongoing during backcrossing cycles. Regions of either high or low introgression tended to be in terminal chromosomal regions that are generally rich in both genes and crossover events, with long stretches around the centromere having limited crossover activity resulting in relatively constant low introgression frequencies. Constraints on fixation and selection of donor alleles highlights the challenges of utilizing introgression breeding in crop improvement.
Collapse
Affiliation(s)
- Jeevan Adhikari
- Plant Genome Mapping Laboratory, Department of Crop and Soil Sciences, University of Georgia, Athens, GA, USA
| | | | - Deepak Vitrakoti
- Plant Genome Mapping Laboratory, Department of Crop and Soil Sciences, University of Georgia, Athens, GA, USA
| | - Sameer Khanal
- Institute of Plant Breeding Genetics and Genomics, Department of Crop and Soil Sciences, University of Georgia, Tifton, GA, USA
| | - Wiriyanat Ployaram
- Plant Genome Mapping Laboratory, Department of Crop and Soil Sciences, University of Georgia, Athens, GA, USA
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, Department of Crop and Soil Sciences, University of Georgia, Athens, GA, USA.
| |
Collapse
|
2
|
Patel JD, Khanal S, Chandnani R, Adhikari J, Brown N, Chee PW, Jones DC, Paterson AH. Improved Upland Cotton Germplasm for Multiple Fiber Traits Mediated by Transferring and Pyramiding Novel Alleles From Ethyl Methanesulfonate-Generated Mutant Lines Into Elite Genotypes. Front Plant Sci 2022; 13:842741. [PMID: 35498694 PMCID: PMC9044065 DOI: 10.3389/fpls.2022.842741] [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: 12/24/2021] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
Ethyl methanesulfonate (EMS) mutagenesis offers important advantages for improving crops, such as cotton, with limited diversity in elite gene pools. EMS-induced point mutations are less frequently associated with deleterious traits than alleles from wild or exotic germplasm. From 157 mutant lines that have significantly improved fiber properties, we focused on nine mutant lines here. A total of eight populations were developed by crossing mutant lines in different combinations into GA230 (GA2004230) background. Multiple lines in each population were significantly improved for the fiber trait that distinguished the donor parent(s), demonstrating that an elite breeding line (GA230) could be improved for fiber qualities using the mutant lines. Genotypes improved for multiple fiber traits of interest suggesting that allele pyramiding is possible. Compared to midparent values, individual progeny in the population conferred fiber quality improvements of as much as 31.7% (in population O) for micronaire (MIC), 16.1% (in population P) for length, 22.4% (in population K) for strength, 4.1% (in population Q) for uniformity, 45.8% (in population N) for elongation, and 13.9% (in population O) for lint percentage (lint%). While further testing for stability of the phenotype and estimation of yield potential is necessary, mutation breeding shows promise as an approach to reduce the problem of the genetic bottleneck of upland cotton. The populations developed here may also contribute to identifying candidate genes and causal mutations for fiber quality improvement.
Collapse
Affiliation(s)
- Jinesh D. Patel
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, United States
| | - Sameer Khanal
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, United States
| | - Rahul Chandnani
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, United States
| | - Jeevan Adhikari
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, United States
| | - Nino Brown
- Department of Crop and Soil Sciences, The University of Georgia, Tifton, GA, United States
- NESPAL Molecular Cotton Breeding Laboratory, The University of Georgia, Tifton, GA, United States
| | - Peng W. Chee
- Department of Crop and Soil Sciences, The University of Georgia, Tifton, GA, United States
| | - Don C. Jones
- Cotton Incorporated, Agricultural Research, Cary, NC, United States
| | - Andrew H. Paterson
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, United States
| |
Collapse
|
3
|
Chandnani R, Kim C, Patel JD, Guo H, Shehzad T, Wallace JG, He D, Zhang Z, Adhikari J, Khanal S, Chee PW, Paterson AH. Identification of small effect quantitative trait loci of plant architectural, flowering, and early maturity traits in reciprocal interspecific introgression population in cotton. Front Plant Sci 2022; 13:981682. [PMID: 36061803 PMCID: PMC9433993 DOI: 10.3389/fpls.2022.981682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 07/26/2022] [Indexed: 05/13/2023]
Abstract
Plant architecture, flowering time and maturity traits are important determinants of yield and fiber quality of cotton. Genetic dissection of loci determining these yield and quality components is complicated by numerous loci with alleles conferring small differences. Therefore, mapping populations segregating for smaller numbers and sizes of introgressed segments is expected to facilitate dissection of these complex quantitative traits. At an advanced stage in the development of reciprocal advanced backcross populations from crosses between elite Gossypium hirsutum cultivar 'Acala Maxxa' (GH) and G. barbadense 'Pima S6' (GB), we undertook mapping of plant architectural traits, flowering time and maturity. A total of 284 BC4F1 and BC4F2 progeny rows, 120 in GH and 164 in GB background, were evaluated for phenotype, with only 4 and 3 (of 7) traits showing significant differences among progenies. Genotyping by sequencing yielded 3,186 and 3,026 SNPs, respectively, that revealed a total of 27 QTLs in GH background and 22 in GB, for plant height, days to flowering, residual flowering at maturity and maturity. More than of 90% QTLs identified in both backgrounds had small effects (%PV < 10), supporting the merit of this population structure to reduce background noise and small effect QTLs. Germplasm developed in this study may serve as potential pre-breeding material to develop improved cotton cultivars.
Collapse
Affiliation(s)
- Rahul Chandnani
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, United States
| | - Changsoo Kim
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, United States
- Department of Crop Science, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, South Korea
| | - Jinesh D. Patel
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, United States
| | - Hui Guo
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, United States
| | - Tariq Shehzad
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, United States
| | - Jason G. Wallace
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
| | - Daohua He
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhengsheng Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Jeevan Adhikari
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, United States
| | - Sameer Khanal
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, United States
| | - Peng W. Chee
- NESPAL Molecular Cotton Breeding Laboratory, The University of Georgia, Tifton, GA, United States
| | - Andrew H. Paterson
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, United States
- *Correspondence: Andrew H. Paterson,
| |
Collapse
|
4
|
Ghosh S, Das M, Basu S, Adhikari J. Gluconeogenic fructose-1,6-bisphosphatase from the mature sporocarps of common aquatic ferns: partial purification and basic characterization of this enzyme from Marsilea minuta (Polypodiopsida). Ukr Bot J 2020. [DOI: 10.15407/ukrbotj77.05.386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The present communication reports substantial activity of gluconeogenic fructose-1,6-bisphosphatase (FBPase; EC 3.1.3.11) in three common heterosporous aquatic ferns (Marsilea minuta, Salvinia natans, and Azolla pinnata) and also describes a protocol for its partial purification from mature sporocarps of Marsilea minuta. The cytosolic FBPase, obtained from Marsilea minuta, Salvinia natans, and Azolla pinnata was recognized as gluconeogenic enzyme due to its drastic catabolic inactivation in presence of externally administered glucose and its insensitivity towards photosynthetic light illumination. Cytosolic gluconeogenic FBPase was partially purified from mature sporocarps of Marsilea minuta to about 22-fold over homogenate following low-speed centrifugation (11, 400 × g), 30–80% ammonium sulfate fractionation followed by subsequent chromatography using matrices like CM-Cellulose, Sephadex G-200, and Ultrogel AcA 34. The profile of partially purified FBPase in PAGE under non-denaturing condition was recorded. The enzyme activity increased linearly with respect to protein concentration to about 100 µg and with respect to time up to 75 minutes. Temperature optimum was found at 35 °C. The effect of substrate concentration and kinetic analyses for FBPase were carried out using D-fructose-1,6-bisphosphate (D-FBP, the substrate) in the range of 0.0 to 1.0 mM at an interval of 0.1 mM concentration. The Km value for D-FBP of FBPase was 0.06129 mM and Vmax was 4525 nmole Pi released (mg)-1 protein h-1 as determined by nonlinear regression kinetics using Prism 8 software (Graph Pad). The enzyme was functional in a constricted pH range of 7.0 to 8.0, giving maxima at pH 7.5. This cytosolic enzyme was significantly stimulated by Mg2+ and strongly inhibited by Hg2+, Cu2+ and Zn2+.
Collapse
|
5
|
Feng Y, Beaton N, Adhikari J, Bruderer R, Tomlinson R, Cornella-Taracido I, Reiter L. High-Resolution Limited Proteolysis (HR-LIP): A novel approach for target validation and lead compound optimization. Eur J Cancer 2020. [DOI: 10.1016/s0959-8049(20)31177-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
6
|
Patel JD, Huang X, Lin L, Das S, Chandnani R, Khanal S, Adhikari J, Shehzad T, Guo H, Roy-Zokan EM, Rong J, Paterson AH. The Ligon lintless -2 Short Fiber Mutation Is Located within a Terminal Deletion of Chromosome 18 in Cotton. Plant Physiol 2020; 183:277-288. [PMID: 32102829 PMCID: PMC7210651 DOI: 10.1104/pp.19.01531] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 01/28/2020] [Indexed: 05/06/2023]
Abstract
Extreme elongation distinguishes about one-fourth of cotton (Gossypium sp.) seed epidermal cells as "lint" fibers, useful for the textile industry, from "fuzz" fibers (<5 mm). Ligon lintless-2 (Li 2 ), a dominant mutation that results in no lint fiber but normal fuzz fiber, offers insight into pathways and mechanisms that differentiate spinnable cotton from its progenitors. A genetic map developed using 1,545 F2 plants showed that marker CISP15 was 0.4 cM from Li 2 , and "dominant" simple sequence repeat (SSR) markers (i.e. with null alleles in the Li 2 genotype) SSR7 and SSR18 showed complete linkage with Li 2 Nonrandom distribution of markers with null alleles suggests that the Li 2 phenotype results from a 176- to 221-kb deletion of the terminal region of chromosome 18 that may have been masked in prior pooled-sample mapping strategies. The deletion includes 10 genes with putative roles in fiber development. Two Glycosyltransferase Family 1 genes showed striking expression differences during elongation of wild-type versus Li 2 fiber, and virus-induced silencing of these genes in the wild type induced Li 2 -like phenotypes. Further, at least 7 of the 10 putative fiber development genes in the deletion region showed higher expression in the wild type than in Li 2 mutants during fiber development stages, suggesting coordinated regulation of processes in cell wall development and cell elongation, consistent with the hypothesis that some fiber-related quantitative trait loci comprise closely spaced groups of functionally diverse but coordinately regulated genes.
Collapse
Affiliation(s)
- Jinesh D Patel
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602
| | - Xianzhong Huang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602
- Plant Genomics Laboratory, College of Life Sciences, Shihezi University, 832003 Shihezi, China
| | - Lifeng Lin
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602
| | - Sayan Das
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602
| | - Rahul Chandnani
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602
| | - Sameer Khanal
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602
| | - Jeevan Adhikari
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602
| | - Tariq Shehzad
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, 2713 Doha, Qatar
| | - Hui Guo
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602
| | - Eileen M Roy-Zokan
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602
| | - Junkang Rong
- Zhejiang A&F University, Linan, Hangzhou 311300, Zhejiang, China
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602
| |
Collapse
|
7
|
Khanal S, Dunne JC, Schwartz BM, Kim C, Milla-Lewis S, Raymer PL, Hanna WW, Adhikari J, Auckland SA, Rainville L, Paterson AH. Molecular Dissection of Quantitative Variation in Bermudagrass Hybrids ( Cynodon dactylon x transvaalensis): Morphological Traits. G3 (Bethesda) 2019; 9:2581-2596. [PMID: 31208957 PMCID: PMC6686926 DOI: 10.1534/g3.119.400061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 06/05/2019] [Indexed: 11/30/2022]
Abstract
Bermudagrass (Cynodon (L.)) is the most important warm-season grass grown for forage or turf. It shows extensive variation in morphological characteristics and growth attributes, but the genetic basis of this variation is little understood. Detection and tagging of quantitative trait loci (QTL) affecting above-ground morphology with diagnostic DNA markers would provide a foundation for genetic and molecular breeding applications in bermudagrass. Here, we report early findings regarding genetic architecture of foliage (canopy height, HT), stolon (stolon internode length, ILEN and length of the longest stolon LLS), and leaf traits (leaf blade length, LLEN and leaf blade width, LW) in 110 F1 individuals derived from a cross between Cynodon dactylon (T89) and C. transvaalensis (T574). Separate and joint environment analyses were performed on trait data collected across two to five environments (locations, and/or years, or time), finding significant differences (P < 0.001) among the hybrid progeny for all traits. Analysis of marker-trait associations detected 74 QTL and 135 epistatic interactions. Composite interval mapping (CIM) and mixed-model CIM (MCIM) identified 32 main effect QTL (M-QTL) and 13 interacting QTL (int-QTL). Colocalization of QTL for plant morphology partially explained significant correlations among traits. M-QTL qILEN-3-2 (for ILEN; R2 = 11-19%), qLLS-7-1 (for LLS; R2 = 13-27%), qLEN-1-1 (for LLEN; R2 = 10-11%), and qLW-3-2 (for LW; R2 = 10-12%) were 'stable' across multiple environments, representing candidates for fine mapping and applied breeding applications. QTL correspondence between bermudagrass and divergent grass lineages suggests opportunities to accelerate progress by predictive breeding of bermudagrass.
Collapse
Affiliation(s)
- Sameer Khanal
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30606
| | - Jeffrey C Dunne
- Crop Science Department, North Carolina State University, Raleigh, NC 27695
| | - Brian M Schwartz
- Department of Crop and Soil Sciences, University of Georgia, Tifton, GA 31794, and
| | - Changsoo Kim
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30606
| | - Susana Milla-Lewis
- Crop Science Department, North Carolina State University, Raleigh, NC 27695
| | - Paul L Raymer
- Department of Crop and Soil Sciences, University of Georgia, Griffin, GA 30224
| | - Wayne W Hanna
- Department of Crop and Soil Sciences, University of Georgia, Tifton, GA 31794, and
| | - Jeevan Adhikari
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30606
| | - Susan A Auckland
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30606
| | - Lisa Rainville
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30606
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30606,
| |
Collapse
|
8
|
Adhikari J, Chambers E, Koppel K. Impact of consumption temperature on sensory properties of hot brewed coffee. Food Res Int 2019; 115:95-104. [DOI: 10.1016/j.foodres.2018.08.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 07/13/2018] [Accepted: 08/02/2018] [Indexed: 11/26/2022]
|
9
|
Sah G, Sapkota A, Adhikari J, Singh J, Pokhrel N. P3.15-25 Assessment of Depression Among Advanced Stage Lung Cancer Patients in Developing Country. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.08.1901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
10
|
Chandnani R, Kim C, Guo H, Shehzad T, Wallace JG, He D, Zhang Z, Patel JD, Adhikari J, Khanal S, Paterson AH. Genetic Analysis of Gossypium Fiber Quality Traits in Reciprocal Advanced Backcross Populations. Plant Genome 2018; 11:241. [PMID: 29505644 DOI: 10.1007/s10681-017-2029-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 09/11/2017] [Indexed: 05/27/2023]
Abstract
In mapping populations segregating for many loci, the large amount of variation among genotypes often masks small-effect quantitative trait loci (QTL). This problem can be reduced by development of populations with fewer chromosome segments segregating. Here, we report early QTL detection in reciprocal advanced backcross populations from crosses between elite Gossypium hirsutum L. 'Acala Maxxa' (GH) and G. barbadense L. 'Pima S6' (GB). A total of 297 BCF and BCF progeny rows-127 segregating for GB chromosome segments in GH background and 170 segregating for GH chromosome segments in GB background-were evaluated in three environments. Totals of 3186 and 3026 polymorphic single-nucleotide polymorphisms (SNPs) in GH and GB backgrounds, respectively, were identified and used for trait mapping. Small-effect QTL (<10% variance explained) made up 87 and 100% of QTL in GH and GB backgrounds, respectively. In both species, favorable alleles were found with effects being masked or neutralized by unfavorable alleles, with greater scope for improvement of GH than GB by introgressive breeding. A total of three stable QTL-two in GH background for fiber elongation (ELO) and micronaire (MIC) and one in GB background for upper-half mean length (UHM)-were identified in two out of three environments. Curiously, only four QTL-three for UHM and one for ELO-showed the expected opposite effects in reciprocal backgrounds, perhaps reflecting the combined consequences of epistasis, small phenotypic effects, and low coverage of some genomic regions. Along with new information for marker-assisted breeding, this study adds to knowledge that can be used to unravel complex genetic networks governing fiber quality traits.
Collapse
|
11
|
Chandnani R, Kim C, Guo H, Shehzad T, Wallace JG, He D, Zhang Z, Patel JD, Adhikari J, Khanal S, Paterson AH. Genetic Analysis of Gossypium Fiber Quality Traits in Reciprocal Advanced Backcross Populations. Plant Genome 2018; 11:170057. [PMID: 29505644 DOI: 10.3835/plantgenome2017.06.0057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In mapping populations segregating for many loci, the large amount of variation among genotypes often masks small-effect quantitative trait loci (QTL). This problem can be reduced by development of populations with fewer chromosome segments segregating. Here, we report early QTL detection in reciprocal advanced backcross populations from crosses between elite Gossypium hirsutum L. 'Acala Maxxa' (GH) and G. barbadense L. 'Pima S6' (GB). A total of 297 BCF and BCF progeny rows-127 segregating for GB chromosome segments in GH background and 170 segregating for GH chromosome segments in GB background-were evaluated in three environments. Totals of 3186 and 3026 polymorphic single-nucleotide polymorphisms (SNPs) in GH and GB backgrounds, respectively, were identified and used for trait mapping. Small-effect QTL (<10% variance explained) made up 87 and 100% of QTL in GH and GB backgrounds, respectively. In both species, favorable alleles were found with effects being masked or neutralized by unfavorable alleles, with greater scope for improvement of GH than GB by introgressive breeding. A total of three stable QTL-two in GH background for fiber elongation (ELO) and micronaire (MIC) and one in GB background for upper-half mean length (UHM)-were identified in two out of three environments. Curiously, only four QTL-three for UHM and one for ELO-showed the expected opposite effects in reciprocal backgrounds, perhaps reflecting the combined consequences of epistasis, small phenotypic effects, and low coverage of some genomic regions. Along with new information for marker-assisted breeding, this study adds to knowledge that can be used to unravel complex genetic networks governing fiber quality traits.
Collapse
|
12
|
Khanal S, Kim C, Auckland SA, Rainville LK, Adhikari J, Schwartz BM, Paterson AH. SSR-enriched genetic linkage maps of bermudagrass (Cynodon dactylon × transvaalensis), and their comparison with allied plant genomes. Theor Appl Genet 2017; 130:819-839. [PMID: 28168408 DOI: 10.1007/s00122-017-2854-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 01/04/2017] [Indexed: 05/20/2023]
Abstract
We report SSR-enriched genetic maps of bermudagrass that: (1) reveal partial residual polysomic inheritance in the tetraploid species, and (2) provide insights into the evolution of chloridoid genomes. This study describes genetic linkage maps of two bermudagrass species, Cynodon dactylon (T89) and Cynodon transvaalensis (T574), that integrate heterologous microsatellite markers from sugarcane into frameworks built with single-dose restriction fragments (SDRFs). A maximum likelihood approach was used to construct two separate parental maps from a population of 110 F1 progeny of a cross between the two parents. The T89 map is based on 291 loci on 34 cosegregating groups (CGs), with an average marker spacing of 12.5 cM. The T574 map is based on 125 loci on 14 CGs, with an average marker spacing of 10.7 cM. Six T89 and one T574 CG(s) deviated from disomic inheritance. Furthermore, marker segregation data and linkage phase analysis revealed partial residual polysomic inheritance in T89, suggesting that common bermudagrass is undergoing diploidization following whole genome duplication (WGD). Twenty-six T89 CGs were coalesced into 9 homo(eo)logous linkage groups (LGs), while 12 T574 CGs were assembled into 9 LGs, both putatively representing the basic chromosome complement (x = 9) of the species. Eight T89 and two T574 CGs remain unassigned. The marker composition of bermudagrass ancestral chromosomes was inferred by aligning T89 and T574 homologs, and used in comparisons to sorghum and rice genome sequences based on 108 and 91 significant blast hits, respectively. Two nested chromosome fusions (NCFs) shared by two other chloridoids (i.e., zoysiagrass and finger millet) and at least three independent translocation events were evident during chromosome number reduction from 14 in the polyploid common ancestor of Poaceae to 9 in Cynodon.
Collapse
Affiliation(s)
- Sameer Khanal
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Changsoo Kim
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
- Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134, South Korea
| | - Susan A Auckland
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Lisa K Rainville
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Jeevan Adhikari
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Brian M Schwartz
- Department of Crop and Soil Sciences, University of Georgia, Tifton, GA, 31793, USA
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA.
| |
Collapse
|
13
|
Dongol S, Shrestha S, Shrestha N, Adhikari J. Clinical Profile and Outcome of Acute Encephalitis Syndrome in Dhulikhel Hospital of Nepal. J Nepal Paedtr Soc 2013. [DOI: 10.3126/jnps.v32i3.6683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction: Acute encephalitis syndrome (AES) is a constellation of clinical signs and or symptoms i.e. acute fever with acute change in mental status. AES may be present as encephalitis, meningoencephalitis or meningitis. It can be associated with severe complication, including impaired consciousness, seizure, limb paresis or death. Materials and Methods: Study consisted of retrospective analysis of hospital records of children up to 16 years of age admitted with diagnosis of AES in the department of Paediatrics Dhulikhel Hospital, Kathmandu University Teaching Hospital, Dhulikhel Kavre from January 2010 to December 2011. Results: During the two years (January 2010 to December 2011), 47 patients of AES were admitted. Among the admitted cases there were 34 male and 13 female patients. Meningitis cases were 29, encephalitis cases were 14 and 4 meningoencephalitis cases. Among the meningitis cases, viral meningitis accounted for 12, bacterial meningitis accounted for 15 and 1 tubercular meningitis.One was eosinopilic meningitis in which the causative organism was found to be fasciolosis by ELISA. Viral encephalitis was found to be the most common cause of encephalitis. Sensorineural hearing loss was seen in 3 cases, subdural effusion in 1 and hydrocephalus in 1. One patient had intracranial hemorrhage with hemiparesis as a complication of eosinophilic meningitis. Conclusion: Acute encephalitis syndrome is one of the most common causes of PICU admission in Dhulikhel hospital. Bacterial meningitis was common among the acute encephalitis syndrome followed by viral meningitis. One case of eosinophilic meningitis with intracranical hemorrhage and hemiparesis was found. Sensorineural hearing loss was found to be commonest complication. DOI: http://dx.doi.org/10.3126/jnps.v32i3.6683 J. Nepal Paediatr. SocVol.32(3) 2012 201-205
Collapse
|
14
|
Singh JK, Adhikari J, Kwak SK. Interfacial properties of Morse fluids. Mol Phys 2007. [DOI: 10.1080/00268970701590193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
15
|
Adhikari J, Kumar A. Study of structural and thermodynamic properties of GaAs and InAs using Monte Carlo simulations. Molecular Simulation 2007. [DOI: 10.1080/08927020701365505] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
16
|
|
17
|
Chhetri DR, Adhikari J, Mukherjee AK. NAD+ mediated differential thermotolerance between chloroplastic and cytosolic L-myo-inositol-1-phosphate synthase from Diplopterygium glaucum (Thunb.) Nakai. Prep Biochem Biotechnol 2006; 36:307-19. [PMID: 16971302 DOI: 10.1080/10826060600912476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Relative thermotolerance of the enzyme, L-myo-inositol-1-phosphate synthase (MIPS; EC: 5.5.1.4), from the chloroplastic and cytosolic sources of Diplopterygium glaucum was studied. The purification involved streptomycin sulphate precipitation, ammonium sulphate fractionation, ion-exchange chromatography, and molecular sieve chromatography. After the final chromatography, 16.62% of chloroplastic and 13.47% of cytosolic MIPS could be recovered. Between 15 degrees C and 55 degrees C, the two forms of MIPS exhibited differential thermal stability, which is related to the presence of the MIPS co-factor, NAD+. Added NAD+ increased the lower thermotolerance of the chloroplastic MIPS and the removal of 'built-in' NAD+ decreased the higher thermal stability of the cytosolic MIPS.
Collapse
Affiliation(s)
- D R Chhetri
- Plant Physiology and Biochemistry Laboratory, Post Graduate Department of Botany, Darjeeling Govt. College, Darjeeling, WB, India.
| | | | | |
Collapse
|
18
|
Chhetri DR, Mukherjee AK, Adhikari J. Myo-inositol content in pteridophytes and the isolation and characterization of L-myo-inositol-1-phosphate synthase from Diplopterygium glaucum. ACTA ACUST UNITED AC 2006. [DOI: 10.1590/s1677-04202006000200005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Myo-inositol is involved in normal growth and development of all living organisms and L-myo-inositol-1-phosphate synthase (MIPS; EC: 5.5.1.4) is responsible for its de novo synthesis. This enzyme has been reported for a number of life forms including plants, animals and bacteria. In the present study free myo-inositol has been detected in the common pteridophytes found in the Darjeeling Himalayas and the enzyme, L-myo-inositol-1-phosphate synthase has been partially purified from Diplopterygium glaucum (Thunb.) Nakai. A crude homogenate from the reproductive pinnules of D. glaucum was subjected to streptomycin sulphate precipitation and 0-70% ammonium sulphate fractionation followed by successive chromatography through DEAE-cellulose, Hexylagarose and BioGel A-0.5m columns. This resulted in a partial purification of the enzyme of about 81-fold with 13.5% recovery. The pteridophytic MIPS specifically utilized D-glucose-6-phosphte and NAD+ as its substrate and co-factor, respectively. It shows a pH optimum between 7.0 and 7.5 while the temperature maximum was 30 °C. The enzyme activity was stimulated by NH4+, slightly inhibited by Na+, Ba2+ and Cd2+, and strongly inhibited by Li+, Zn2+ and Hg2+. EDTA, pCMB and some substrate isomers like glucose-1-phosphate, fructose-6-phosphte and galactose-6-phosphate were inhibitory to the enzyme. The apparent molecular weight of the native D. glaucum MIPS was determined to be approximately 171 kDa.
Collapse
Affiliation(s)
| | - A. K. Mukherjee
- Bengal College of Engineering and Technology Bidhan Nagar, India
| | | |
Collapse
|
19
|
Adhikari J, Böhle HG. Urbanization, government policies and growing food insecurity in Kathmandu metropolis. Stud Nepali Hist Soc 1999; 4:191-246. [PMID: 22462111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
|
20
|
Affiliation(s)
- S. Adhikari
- Ganesh Scientific Research Foundation; 64-65, Najafgarh Road New Delhi 110015 India
| | - J. Adhikari
- Ganesh Scientific Research Foundation; 64-65, Najafgarh Road New Delhi 110015 India
| |
Collapse
|
21
|
Banerjee J, Banerjee S, Adhikari J. Phosphoinositides from human foetal brain during development. J Indian Med Assoc 1989; 87:6-8. [PMID: 2546993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
An attempt has been made in the present study to look for the activity of the enzymes which catalyse the breakdown of phosphorylated metabolites both in acidic and alkaline pH from human foetal brain, in different gestational ages during development in 18 foetal samples. It was revealed that phosphatases were distributed throughout the brain and were operative from the onset of development. There was a tendency of increment of specific activity of enzymes with respect to the advancement of gestational period. This observation should be accounted as a prerequisite criteria for understanding phosphate meatabolism in human foetal organs primarily associated with glycolytic and gluconeogenic pathways.
Collapse
|
22
|
Adhikari J, Majumder AL. L-myo-inositol-1-phosphate synthase from mammalian brain: partial purification and characterisation of the fetal and adult enzyme. Indian J Biochem Biophys 1988; 25:408-12. [PMID: 3243558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|
23
|
Adhikari J, Majumder AL, Bhaduri TJ, Dasgupta S, Majumder AL. Chloroplast as a Locale of L-myo-Inositol-1-Phosphate Synthase. Plant Physiol 1987; 85:611-4. [PMID: 16665747 PMCID: PMC1054309 DOI: 10.1104/pp.85.3.611] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Chloroplasts from 5 to 7 day old Vigna radiata seedling, grown under alternate light/dark conditions or from green Euglena gracilis Z. cells have been found to harbor L-myo-inositol-1-phosphate synthase (EC 5.5.1.4) activity. In contrast, dark-grown V. radiata seedlings, or streptomycin-bleached Euglena cells exhibit either reduced or no enzyme activity. An apparent enhancement of the chloroplastic inositol synthase by growth in presence of light is observed.
Collapse
Affiliation(s)
- J Adhikari
- Biochemistry Laboratory, Department of Botany, Visva Bharati University, Santiniketan, 731235, India
| | | | | | | | | |
Collapse
|
24
|
Adhikari J, Majumder AL. Differences in thermal stability of the fetal and adult brain myoinositol-1-phosphate synthase. Probable involvement of NAD. FEBS Lett 1983; 163:46-9. [PMID: 6628688 DOI: 10.1016/0014-5793(83)81159-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
L-myo-inositol-1-phosphate synthase (EC 5.5.1.4) from mammalian fetal and adult brain differ considerably with respect to their stability towards different temperatures between 25-65 degrees C. This property has been found to be associated with the presence of the synthase co-factor, NAD, bound to the enzyme protein. The lower thermal stability of the fetal enzyme increases in presence of added NAD (0.8 mM) whereas the higher thermal stability of the adult brain enzyme declines when NAD is specifically removed from the enzyme.
Collapse
|
25
|
Biswas T, Adhikari J, Choudhuri RB, Majumder AL. Fructose-1,6-bisphosphatase & myo-inositol synthase: a phylogenetic search. Indian J Biochem Biophys 1981; 18:442-4. [PMID: 6277770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|