1
|
Li G, Che J, Gong J, Duan L, Zhang Z, Jiang X, Xu P, Fan S, Gong W, Shi Y, Liu A, Li J, Li P, Pan J, Deng X, Yuan Y, Shang H. Quantitative Trait Locus Mapping for Plant Height and Branch Number in CCRI70 Recombinant Inbred Line Population of Upland Cotton (Gossypium hirsutum). PLANTS (BASEL, SWITZERLAND) 2024; 13:1509. [PMID: 38891318 PMCID: PMC11174691 DOI: 10.3390/plants13111509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/08/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024]
Abstract
Upland cotton accounts for a high percentage (95%) of the world's cotton production. Plant height (PH) and branch number (BN) are two important agronomic traits that have an impact on improving the level of cotton mechanical harvesting and cotton yield. In this research, a recombinant inbred line (RIL) population with 250 lines developed from the variety CCRI70 was used for constructing a high-density genetic map and identification of quantitative trait locus (QTL). The results showed that the map harbored 8298 single nucleotide polymorphism (SNP) markers, spanning a total distance of 4876.70 centimorgans (cMs). A total of 69 QTLs for PH (9 stable) and 63 for BN (11 stable) were identified and only one for PH was reported in previous studies. The QTLs for PH and BN harbored 495 and 446 genes, respectively. Combining the annotation information, expression patterns and previous studies of these genes, six genes could be considered as potential candidate genes for PH and BN. The results could be helpful for cotton researchers to better understand the genetic mechanism of PH and BN development, as well as provide valuable genetic resources for cotton breeders to manipulate cotton plant architecture to meet future demands.
Collapse
Affiliation(s)
- Gangling Li
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (G.L.); (J.C.)
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
| | - Jincan Che
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (G.L.); (J.C.)
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Juwu Gong
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
| | - Li Duan
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory of Plant Stress Biology, College of Life Science, Henan University, Kaifeng 475001, China
| | - Zhen Zhang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
| | - Xiao Jiang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
| | - Peng Xu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
| | - Senmiao Fan
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
| | - Wankui Gong
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
| | - Yuzhen Shi
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
| | - Aiying Liu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
| | - Junwen Li
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
| | - Pengtao Li
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
| | - Jingtao Pan
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
| | - Xiaoying Deng
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
| | - Youlu Yuan
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (G.L.); (J.C.)
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
| | - Haihong Shang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (G.L.); (J.C.)
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
| |
Collapse
|
2
|
Singh J, Sharma A, Sharma V, Gaikwad PN, Sidhu GS, Kaur G, Kaur N, Jindal T, Chhuneja P, Rattanpal HS. Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species. Sci Rep 2023; 13:10919. [PMID: 37407627 DOI: 10.1038/s41598-023-37024-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 06/14/2023] [Indexed: 07/07/2023] Open
Abstract
Citrus species among the most important and widely consumed fruit in the world due to Vitamin C, essential oil glands, and flavonoids. Highly variable simple sequence repeats (SSR) markers are one of the most informative and versatile molecular markers used in perennial tree genetic research. SSR survey of Citrus sinensis and Citrus maxima were identified perfect SSRs spanning nine chromosomes. Furthermore, we categorized all SSR motifs into three major classes based on their tract lengths. We designed and validated a class I SSRs in the C. sinensis and C. maxima genome through electronic polymerase chain reaction (ePCR) and found 83.89% in C. sinensis and 78.52% in C. maxima SSRs producing a single amplicon. Then, we selected extremely variable SSRs (> 40 nt) from the ePCR-verified class I SSRs and in silico validated across seven draft genomes of citrus, which provided us a subset of 84.74% in C. sinensis and 77.53% in C. maxima highly polymorphic SSRs. Out of these, 129 primers were validated on 24 citrus genotypes through wet-lab experiment. We found 127 (98.45%) polymorphic HvSSRs on 24 genotypes. The utility of the developed HvSSRs was demonstrated by analysing genetic diversity of 181 citrus genotypes using 17 HvSSRs spanning nine citrus chromosomes and were divided into 11 main groups through 17 HvSSRs. These chromosome-specific SSRs will serve as a powerful genomic tool used for future QTL mapping, molecular breeding, investigation of population genetic diversity, comparative mapping, and evolutionary studies among citrus and other relative genera/species.
Collapse
Affiliation(s)
- Jagveer Singh
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
- Department of Fruit Science, College of Horticulture & Forestry, Acharya Narendra Deva University of Agricultural & Technology, Kumarganj, 224229, India
| | - Ankush Sharma
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Vishal Sharma
- National Agri-Food Biotechnology Institute, Sector-81, SAS Nagar, Mohali, Punjab, 140308, India
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, 173229, India
| | - Popat Nanaso Gaikwad
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Gurupkar Singh Sidhu
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India.
| | - Gurwinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Nimarpreet Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Taveena Jindal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - H S Rattanpal
- Department of Fruit Science, Punjab Agricultural University, Ludhiana, 141004, India
| |
Collapse
|
3
|
Shehzad M, Ditta A, Cai X, Ur Rahman S, Xu Y, Wang K, Zhou Z, Fang L. Identification of salt stress-tolerant candidate genes in the BC 2F 2 population at the seedling stages of G. hirsutum and G. darwinii using NGS-based bulked segregant analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1125805. [PMID: 37465381 PMCID: PMC10350501 DOI: 10.3389/fpls.2023.1125805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 05/02/2023] [Indexed: 07/20/2023]
Abstract
Salinity is a major threat to the yield and productivity of cotton seedlings. In the present study, we developed a BC2F2 population of cotton plants from Gossypium darwinii (5-7) and Gossypium hirsutum (CCRI 12-4) salt-susceptible parents to identify salt-resistant candidate genes. The Illumina HiSeq™ strategy was used with bulked segregant analysis. Salt-resistant and salt-susceptible DNA bulks were pooled by using 30 plants from a BC2F2 population. Next-generation sequencing (NGS) technology was used for the sequencing of parents and both bulks. Four significant genomic regions were identified: the first genomic region was located on chromosome 18 (1.86 Mb), the second and third genomic regions were on chromosome 25 (1.06 Mb and 1.94 Mb, respectively), and the fourth was on chromosome 8 (1.41 Mb). The reads of bulk1 and bulk2 were aligned to the G. darwinii and G. hirsutum genomes, respectively, leading to the identification of 20,664,007 single-nucleotide polymorphisms (SNPs) and insertions/deletions (indels). After the screening, 6,573 polymorphic markers were obtained after filtration of the candidate regions. The SNP indices in resistant and susceptible bulks and Δ(SNP-index) values of resistant and susceptible bulks were measured. Based on the higher Δ(SNP-index) value, six effective polymorphic SNPs were selected in a different chromosome. Six effective SNPs were linked to five candidate genes in four genomic regions. Further validation of these five candidate genes was carried out using reverse transcription-quantitative polymerase chain reaction (RT-qPCR), resulting in an expression profile that showed two highly upregulated genes in the salt-tolerant species G. darwinii, i.e., Gohir.D05G367800 and Gohir.D12G239100; however, the opposite was shown in G. hirsutum, for which all genes, except one, showed partial expression. The results indicated that Gohir.D05G367800 and Gohir.D12G239100 may be salt-tolerant genes. We are confident that this study could be helpful for the cloning, transformation, and development of salt-resistant cotton varieties.
Collapse
Affiliation(s)
- Muhammad Shehzad
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Allah Ditta
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
- Plant Breeding and Genetics Division, Cotton Group, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, Punjab, Pakistan
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
- National Nanfan Research Institute of Chinese Academy of Agriculture Sciences, Sanya, China
| | - Shafeeq Ur Rahman
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
- National Nanfan Research Institute of Chinese Academy of Agriculture Sciences, Sanya, China
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Liu Fang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
- National Nanfan Research Institute of Chinese Academy of Agriculture Sciences, Sanya, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| |
Collapse
|
4
|
Rasool A, Azeem F, Ur-Rahman M, Rizwan M, Hussnain Siddique M, Bay DH, Binothman N, Al Kashgry NAT, Qari SH. Omics-assisted characterization of two-component system genes from Gossypium Raimondii in response to salinity and molecular interaction with abscisic acid. FRONTIERS IN PLANT SCIENCE 2023; 14:1138048. [PMID: 37063177 PMCID: PMC10102465 DOI: 10.3389/fpls.2023.1138048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/09/2023] [Indexed: 06/19/2023]
Abstract
The two-component system (TCS) genes are involved in a wide range of physiological processes in prokaryotes and eukaryotes. In plants, the TCS elements help in a variety of functions, including cell proliferation, response to abiotic and biotic stresses, leaf senescence, nutritional signaling, and division of chloroplasts. Three different kinds of proteins make up the TCS system in plants. These are known as HKs (histidine kinases), HPs (histidine phosphotransfer), and RRs (response regulators). We investigated the genome of Gossypium raimondii and discovered a total of 59 GrTCS candidates, which include 23 members of the HK family, 8 members of the HP family, and 28 members of the RR family. RR candidates are further classified as type-A (6 members), type-B (11 members), type-C (2 members), and pseudo-RRs (9 members). The GrTCS genes were analyzed in comparison with the TCS components of other plant species such as Arabidopsis thaliana, Cicer arietinum, Sorghum bicolor, Glycine max, and Oryza sativa. This analysis revealed both conservation and changes in their structures. We identified 5 pairs of GrTCS syntenic homologs in the G. raimondii genome. All 59 TCS genes in G. raimondii are located on all thirteen chromosomes. The GrTCS promoter regions have several cis-regulatory elements, which function as switches and respond to a wide variety of abiotic stresses. RNA-seq and real-time qPCR analysis showed that the majority of GrTCS genes are differentially regulated in response to salt and cold stress. 3D structures of GrTCS proteins were predicted to reveal the specific function. GrTCSs were docked with abscisic acid to assess their binding interactions. This research establishes the groundwork for future functional studies of TCS elements in G. raimondii, which will further focus on stress resistance and overall development.
Collapse
Affiliation(s)
- Asima Rasool
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Mahmood Ur-Rahman
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Rizwan
- Department of Environmental Sciences, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Hussnain Siddique
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Daniyah Habiballah Bay
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Najat Binothman
- Department of Chemistry, College of Sciences & Arts, King Abdulaziz University, Rabigh, Saudi Arabia
| | | | - Sameer H. Qari
- Department of Biology, A1-Jumum University College, Umm A1-Qura University, Makkah, Saudi Arabia
| |
Collapse
|
5
|
Transcriptomics for Drought Stress Mediated by Biological Processes in-relation to Key Regulated Pathways in Gossypium darwinii. Mol Biol Rep 2022; 49:11341-11350. [PMID: 35907118 DOI: 10.1007/s11033-022-07774-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/05/2022] [Indexed: 10/16/2022]
Abstract
BACKGROUND Wild cotton Gossypium darwinii, an allotetraploid harbours important traits useful for tolerating abiotic stress, i.e., drought, salt and good genetic stability, hence these characteristics can be transferred to cultivated cotton for genetic improvement. MATERIALS AND METHODS In this study, we analyzed the RNA-seq transcriptomes from leaves of G. darwinii seedlings with and without drought stress. A total of 86.7 million valid reads with an average length of 95.79 bp were generated from the two samples and 58,960 transcripts with a length of more than 500 bp were assembled. We searched the known proteins on the strength of sequence similarity; these transcripts were annotated with COG, KEGG and GO functional categories. According to gene expression abundance RPKM value, we carried out RT-qPCR analysis to determine the expression pattern of the obtained transcription factors. RESULTS A total of 58,960 genes was differentially expressed (DEG), with 32,693 and 25,919 genes found to be upregulated and downregulated, respectively. Through gene ontology and KEGG pathways, the upregulated genes were found to associate with all the GO terms, molecular functions (MF), biological process (BP) and cellular components (CC), which are highly linked to enhancing drought stress tolerance. CONCLUSION The study provides an in-depth knowledge of regulation of pathways and genes involved in photosynthesis during drought stress in G. darwinii. These pathways and genes were found to be significantly downregulated and this information could be further utilized by cotton breeders in developing a more drought tolerant cotton germplasm.
Collapse
|
6
|
Boiko S. Design of microsatellite markers for Schizophyllum commune (Agaricales, Basidiomycota) based on analysis of its genome. UKRAINIAN BOTANICAL JOURNAL 2022. [DOI: 10.15407/ukrbotj79.01.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Simple sequence repeats of DNA (SSRs) are the most popular source of genetic markers used in population genetics, phylogenetics, and genetic mapping. A large number of nucleotide repeats enriched in G and C were identified. 336 mononucleotide motifs with more than ten repeats were recorded. 2020 nucleotide repeats were identified, of which 97.4% are di- (68.2%) and trinucleotides (29.2%). The total number of unique SSR loci, to which primers pairs were developed, was 1920. PCR primer sequences for unique SSR loci of the S. commune genome are presented. Of the twenty-two SSR markers synthesized for the S. commune genome, amplicons formed 64% on freshly isolated DNA samples.
Collapse
|
7
|
Azeem F, Zameer R, Rehman Rashid MA, Rasul I, Ul-Allah S, Siddique MH, Fiaz S, Raza A, Younas A, Rasool A, Ali MA, Anwar S, Siddiqui MH. Genome-wide analysis of potassium transport genes in Gossypium raimondii suggest a role of GrHAK/KUP/KT8, GrAKT2.1 and GrAKT1.1 in response to abiotic stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 170:110-122. [PMID: 34864561 DOI: 10.1016/j.plaphy.2021.11.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
Potassium (K+) is an important macro-nutrient for plants, which comprises almost 10% of plant's dry mass. It plays a crucial role in the growth of plants as well as other important processes related to metabolism and stress tolerance. Plants have a complex and well-organized potassium distribution system (channels and transporters). Cotton is the most important economic crop, which is the primary source of natural fiber. Soil deficiency in K+ can negatively affect yield and fiber quality of cotton. However, potassium transport system in cotton is poorly studied. Current study identified 43 Potassium Transport System (PTS) genes in Gossypium raimondii genome. Based on conserved domains, transmembrane domains, and motif structures, these genes were classified as K+ transporters (2 HKTs, 7 KEAs, and 16 KUP/HAK/KTs) and K+ channels (11 Shakers and 7 TPKs/KCO). The phylogenetic comparison of GrPTS genes from Arabidopsis thaliana, Glycine max, Oryza sativa, Medicago truncatula and Cicer arietinum revealed variations in PTS gene conservation. Evolutionary analysis predicted that most GrPTS genes were segmentally duplicated. Gene structure analysis showed that the intron/exon organization of these genes was conserved in specific-family. Chromosomal localization demonstrated a random distribution of PTS genes across all the thirteen chromosomes except chromosome six. Many stress responsive cis-regulatory elements were predicted in promoter regions of GrPTS genes. The RNA-seq data analysis followed by qRT-PCR validation demonstrated that PTS genes potentially work in groups against environmental factors. Moreover, a transporter gene (GrHAK/KUP/KT8) and two channel genes (GrAKT2.1 and GrAKT1.1) are important candidate genes for plant stress response. These results provide useful information for further functional characterization of PTS genes with the breeding aim of stress-resistant cultivars.
Collapse
Affiliation(s)
- Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Govt. College University, Faisalabad, Pakistan
| | - Roshan Zameer
- Department of Bioinformatics and Biotechnology, Govt. College University, Faisalabad, Pakistan
| | | | - Ijaz Rasul
- Department of Bioinformatics and Biotechnology, Govt. College University, Faisalabad, Pakistan
| | - Sami Ul-Allah
- College of Agriculture, Bahauddin Zakariya University, Bahadur Sub-Campus, Layyah, Pakistan
| | | | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, 22620, Haripir, Pakistan.
| | - Ali Raza
- Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, Fujian, 350002, China
| | - Afifa Younas
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Asima Rasool
- Department of Bioinformatics and Biotechnology, Govt. College University, Faisalabad, Pakistan
| | - Muhammad Amjad Ali
- Department of Plant Pathology, University of Agriculture, Faisalabad, Pakistan
| | - Sultana Anwar
- Department of Agronomy, University of Florida, Gainesville, USA
| | - Manzer H Siddiqui
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| |
Collapse
|
8
|
Mehari TG, Xu Y, Umer MJ, Shiraku ML, Hou Y, Wang Y, Yu S, Zhang X, Wang K, Cai X, Zhou Z, Liu F. Multi-Omics-Based Identification and Functional Characterization of Gh_A06G1257 Proves Its Potential Role in Drought Stress Tolerance in Gossypium hirsutum. FRONTIERS IN PLANT SCIENCE 2021; 12:746771. [PMID: 34745180 PMCID: PMC8567990 DOI: 10.3389/fpls.2021.746771] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 08/31/2021] [Indexed: 05/08/2023]
Abstract
Cotton is one of the most important fiber crops globally. Despite this, various abiotic stresses, including drought, cause yield losses. We used transcriptome profiles to investigate the co-expression patterns of gene networks associated with drought stress tolerance. We identified three gene modules containing 3,567 genes highly associated with drought stress tolerance. Within these modules, we identified 13 hub genes based on intramodular significance, for further validation. The yellow module has five hub genes (Gh_A07G0563, Gh_D05G0221, Gh_A05G3716, Gh_D12G1438, and Gh_D05G0697), the brown module contains three hub genes belonging to the aldehyde dehydrogenase (ALDH) gene family (Gh_A06G1257, Gh_A06G1256, and Gh_D06G1578), and the pink module has five hub genes (Gh_A02G1616, Gh_D12G2599, Gh_D07G2232, Gh_A02G0527, and Gh_D07G0629). Based on RT-qPCR results, the Gh_A06G1257 gene has the highest expression under drought stress in different plant tissues and it might be the true candidate gene linked to drought stress tolerance in cotton. Silencing of Gh_A06G1257 in cotton leaves conferred significant sensitivity in response to drought stress treatments. Overexpression of Gh_A06G1257 in Arabidopsis also confirms its role in drought stress tolerance. L-valine, Glutaric acid, L-proline, L-Glutamic acid, and L-Tryptophan were found to be the most significant metabolites playing roles in drought stress tolerance. These findings add significantly to existing knowledge of drought stress tolerance mechanisms in cotton.
Collapse
Affiliation(s)
- Teame Gereziher Mehari
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Muhammad Jawad Umer
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Margaret Linyerera Shiraku
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yuqing Hou
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yuhong Wang
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Fang Liu
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Anyang, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| |
Collapse
|
9
|
Shehzad M, Zhou Z, Ditta A, Khan M, Cai X, Xu Y, Maqbool A, Khalofah A, Shaban M, Naeem M, Ansari MJ, Wang K, Liu F. Identification and characterization of genes related to salt stress tolerance within segregation distortion regions of genetic map in F2 population of upland cotton. PLoS One 2021; 16:e0247593. [PMID: 33770112 PMCID: PMC7997035 DOI: 10.1371/journal.pone.0247593] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/09/2021] [Indexed: 12/12/2022] Open
Abstract
Segregation distortion (SD) is a genetic mechanism commonly found in segregating or stable populations. The principle behind this puzzles many researchers. The F2 generation developed from wild Gossypium darwinii and G. hirsutum CCRI12 species was used to investigate the possible transcription factors within the segregation distortion regions (SDRs). The 384 out of 2763 markers were distorted in 29 SDRs on 18 chromosomes. Good collinearity was observed among genetic and physical maps of G. hirsutum and G. barbadense syntenic blocks. Total 568 genes were identified from SDRs of 18 chromosomes. Out of these genes, 128 belonged to three top-ranked salt-tolerant gene families. The DUF597 contained 8 uncharacterized genes linked to Pkinase (PF00069) gene family in the phylogenetic tree, while 15 uncharacterized genes clustered with the zinc finger gene family. Two hundred thirty four miRNAs targeted numerous genes, including ghr-miR156, ghr-miR399 and ghr-miR482, while others targeted top-ranked stress-responsive transcription factors. Moreover, these genes were involved in the regulation of numerous stress-responsive cis-regulatory elements. The RNA sequence data of fifteen upregulated genes were verified through the RT-qPCR. The expression profiles of two highly upregulated genes (Gh_D01G2015 and Gh_A01G1773) in salt-tolerant G. darwinii showed antagonistic expression in G. hirsutum. The results indicated that salt-tolerant genes have been possibly transferred from the wild G. darwinii species. A detailed functional analysis of these genes can be carried out which might be helpful in the future for gene cloning, transformation, gene editing and the development of salt-resistant cotton varieties.
Collapse
Affiliation(s)
- Muhammad Shehzad
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
| | - Allah Ditta
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
- Plant Breeding, and Genetics Division, Cotton Group, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, Punjab, Pakistan
| | - Majid Khan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
| | - Amir Maqbool
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Ahlam Khalofah
- Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | - Muhammad Shaban
- Department of Plant Breeding and Genetics, Faculty of Agricultural Science & Technology, Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Naeem
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Mohammad Javed Ansari
- Department of Botany, Hindu College Moradabad (Mahatma Jyotiba Phule Rohilkhand University Bareilly), Bareilly, India
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
- * E-mail: (KW); (FL)
| | - Fang Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- * E-mail: (KW); (FL)
| |
Collapse
|
10
|
Shiraku ML, Magwanga RO, Cai X, Kirungu JN, Xu Y, Mehari TG, Hou Y, Wang Y, Agong SG, Peng R, Wang K, Zhou Z, Liu F. Functional Characterization of GhACX3 Gene Reveals Its Significant Role in Enhancing Drought and Salt Stress Tolerance in Cotton. FRONTIERS IN PLANT SCIENCE 2021; 12:658755. [PMID: 34447398 PMCID: PMC8382881 DOI: 10.3389/fpls.2021.658755] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/17/2021] [Indexed: 05/03/2023]
Abstract
The acyl-coenzyme A oxidase 3 (ACX3) gene involved in the β-oxidation pathway plays a critical role in plant growth and development as well as stress response. Earlier on, studies focused primarily on the role of β-oxidation limited to fatty acid breakdown. However, ACX3 peroxisomal β-oxidation pathways result in a downstream cascade of events that act as a transduction of biochemical and physiological responses to stress. A role that is yet to be studied extensively. In this study, we identified 20, 18, 22, 23, 20, 11, and 9 proteins in Gossypium hirsutum, G. barbadense, G. tomentosum, G. mustelinum, G. darwinii, G. arboretum, and G. raimondii genomes, respectively. The tetraploid cotton genome had protein ranging between 18 and 22, while diploids had between 9 and 11. After analyzing the gene family evolution or selection pressure, we found that this gene family undergoes purely segmental duplication both in diploids and tetraploids. W-Box (WRKY-binding site), ABRE, CAAT-Box, TATA-box, MYB, MBS, LTR, TGACG, and CGTCA-motif are abiotic stress cis-regulatory elements identified in this gene family. All these are the binding sites for abiotic stress transcription factors, indicating that this gene is essential. Genes found in G. hirsutum showed a clear response to drought and salinity stress, with higher expression under drought and salt stress, particularly in the leaf and root, according to expression analysis. We selected Gh_DO1GO186, one of the highly expressed genes, for functional characterization. We functionally characterized the GhACX3 gene through overexpression and virus-induced gene silencing (VIGS). Overexpression of this gene enhanced tolerance under stress, which was exhibited by the germination assay. The overexpressed seed growth rate was faster relative to control under drought and salt stress conditions. The survival rate was also higher in overexpressed plants relative to control plants under stress. In contrast, the silencing of the GhACX3 gene in cotton plants resulted in plants showing the stress susceptibility phenotype and reduced root length compared to control. Biochemical analysis also demonstrated that GhACX3-silenced plants experienced oxidative stress while the overexpressed plants did not. This study has revealed the importance of the ACX3 family during stress tolerance and can breed stress-resilient cultivar.
Collapse
Affiliation(s)
- Margaret L. Shiraku
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Richard Odongo Magwanga
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- School of Biological and Physical Sciences (SBPS), Main Campus, Jaramogi Oginga Odinga University of Science and Technology (JOOUST), Bondo, Kenya
| | - Xiaoyan Cai
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Joy Nyangasi Kirungu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yanchao Xu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Teame Gereziher Mehari
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yuqing Hou
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yuhong Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Stephen Gaya Agong
- School of Biological and Physical Sciences (SBPS), Main Campus, Jaramogi Oginga Odinga University of Science and Technology (JOOUST), Bondo, Kenya
| | - Renhai Peng
- Anyang Institute of Technology, Anyang, China
| | - Kunbo Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zhongli Zhou
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- *Correspondence: Zhongli Zhou,
| | - Fang Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Fang Liu,
| |
Collapse
|
11
|
Patil PG, Singh NV, Bohra A, Raghavendra KP, Mane R, Mundewadikar DM, Babu KD, Sharma J. Comprehensive Characterization and Validation of Chromosome-Specific Highly Polymorphic SSR Markers From Pomegranate ( Punica granatum L.) cv. Tunisia Genome. FRONTIERS IN PLANT SCIENCE 2021; 12:645055. [PMID: 33796127 PMCID: PMC8007985 DOI: 10.3389/fpls.2021.645055] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/12/2021] [Indexed: 05/05/2023]
Abstract
The simple sequence repeat (SSR) survey of 'Tunisia' genome (296.85 Mb) identified a total of 365,279 perfect SSRs spanning eight chromosomes, with a mean marker density of 1,230.6 SSRs/Mb. We found a positive trend in chromosome length and the SSR abundance as marker density enhanced with a shorter chromosome length. The highest number of SSRs (60,708) was mined from chromosome 1 (55.56 Mb), whereas the highest marker density (1,294.62 SSRs/Mb) was recorded for the shortest chromosome 8 (27.99 Mb). Furthermore, we categorized all SSR motifs into three major classes based on their tract lengths. Across the eight chromosomes, the class III had maximum number of SSR motifs (301,684, 82.59%), followed by the class II (31,056, 8.50%) and the class I (5,003, 1.37%). Examination of the distribution of SSR motif types within a chromosome suggested the abundance of hexanucleotide repeats in each chromosome followed by dinucleotides, and these results are consistent with 'Tunisia' genome features as a whole. Concerning major repeat types, AT/AG was the most frequent (14.16%), followed by AAAAAT/AAAAAG (7.89%), A/C (7.54%), AAT/AAG (5.23%), AAAT/AAAG (4.37%), and AAAAT/AAAAG (1.2%) types. We designed and validated a total of 3,839 class I SSRs in the 'Tunisia' genome through electronic polymerase chain reaction (ePCR) and found 1,165 (30.34%) SSRs producing a single amplicon. Then, we selected 906 highly variable SSRs (> 40 nt) from the ePCR-verified class I SSRs and in silico validated across multiple draft genomes of pomegranate, which provided us a subset of 265 highly polymorphic SSRs. Of these, 235 primers were validated on six pomegranate genotypes through wet-lab experiment. We found 221 (94%) polymorphic SSRs on six genotypes, and 187 of these SSRs had ≥ 0.5 PIC values. The utility of the developed SSRs was demonstrated by analyzing genetic diversity of 30 pomegranate genotypes using 16 HvSSRs spanning eight pomegranate chromosomes. In summary, we developed a comprehensive set of highly polymorphic genome-wide SSRs. These chromosome-specific SSRs will serve as a powerful genomic tool to leverage future genetic studies, germplasm management, and genomics-assisted breeding in pomegranate.
Collapse
Affiliation(s)
- Prakash Goudappa Patil
- ICAR-National Research Centre on Pomegranate, Solapur, India
- *Correspondence: Prakash Goudappa Patil,
| | | | | | | | - Rushikesh Mane
- ICAR-National Research Centre on Pomegranate, Solapur, India
| | | | | | - Jyotsana Sharma
- ICAR-National Research Centre on Pomegranate, Solapur, India
| |
Collapse
|
12
|
Li J, Ye C. Genome-wide analysis of microsatellite and sex-linked marker identification in Gleditsia sinensis. BMC PLANT BIOLOGY 2020; 20:338. [PMID: 32680463 PMCID: PMC7367340 DOI: 10.1186/s12870-020-02551-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 07/12/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Gleditsia sinensis Lam. (Leguminosae), a dioecious perennial arbor, demonstrates important medicinal properties and economic value. These properties can be harnessed depending on the sex of the plant. However, the sex of the plants is difficult to identify accurately through morphological methods before the flowering. RESULTS We used bulked segregant analysis to screen sex-specific simple sequence repeat (SSR) markers in G. sinensis. Five male and five female plants were pooled to form the male and female bulks, respectively, and subjected to whole-genome sequencing. After high-throughput sequencing, 5,350,359 sequences were obtained, in which 2,065,210 SSRs were searched. Among them, the number of duplicated SSRs was the highest. The male plants could reach 857,874, which accounted for 60.86% of the total number of male plants. The female plants could reach 1,447,603, which accounted for 56.25% of the total model of the female plants. Among all the nucleotide repeat types, the A/T-rich motif was the most abundant. A total of 309,516 female strain-specific SSRs were selected by clustering. After designing the primers, the male and female gene pools were amplified, and five pairs of primers (i.e., 27, 34, 36, 39, and 41) were found to amplify the differential bands in the male and female gene pools. Using the five pairs of primers, we performed PCR verification on 10 individuals of known sex, which constructed the gene pool. The female plants amplified a single fragment of lengths (i.e., 186, 305, 266, 203, and 260 bp) and no male plant strip, thereby completing the identification of the male and female sexes of the G. sinensis. CONCLUSIONS This study provides accurate sex identification strategies between female and male plants, thus improving the utilization rate of G. sinensis resources.
Collapse
Affiliation(s)
- Jianjun Li
- College of Life Science, Henan Normal University, Green Medicine Biotechnology Henan Engineering Laboratory, Engineering Technology Research Center of Nursing and Utilization of Genuine Chinese Crude Drugs in Henan Province, Xinxiang, 453007 China
| | - Chenglin Ye
- College of Life Science, Henan Normal University, Green Medicine Biotechnology Henan Engineering Laboratory, Engineering Technology Research Center of Nursing and Utilization of Genuine Chinese Crude Drugs in Henan Province, Xinxiang, 453007 China
| |
Collapse
|
13
|
Gupta A, Jaiswal V, Sawant SV, Yadav HK. Mapping QTLs for 15 morpho-metric traits in Arabidopsis thaliana using Col-0 × Don-0 population. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1021-1034. [PMID: 32377050 PMCID: PMC7196571 DOI: 10.1007/s12298-020-00800-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 01/24/2020] [Accepted: 03/17/2020] [Indexed: 05/13/2023]
Abstract
Genome wide quantitative trait loci (QTL) mapping was conducted in Arabidopsis thaliana using F2 mapping population (Col-0 × Don-0) and SNPs markers. A total of five linkage groups were obtained with number of SNPs varying from 45 to 59 per linkage group. The composite interval mapping detected a total of 36 QTLs for 15 traits and the number of QTLs ranged from one (root length, root dry biomass, cauline leaf width, number of internodes and internode distance) to seven (for bolting days). The range of phenotypic variance explained (PVE) and logarithm of the odds ratio of these 36 QTLs was found be 0.19-38.17% and 3.0-6.26 respectively. Further, the epistatic interaction detected one main effect QTL and four epistatic QTLs. Five major QTLs viz. Qbd.nbri.4.3, Qfd.nbri.4.2, Qrdm.nbri.5.1, Qncl.nbri.2.2, Qtd.nbri.4.1 with PVE > 15.0% might be useful for fine mapping to identify genes associated with respective traits, and also for development of specialized population through marker assisted selection. The identification of additive and dominant effect QTLs and desirable alleles of each of above mentioned traits would also be important for future research.
Collapse
Affiliation(s)
- Astha Gupta
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, UP 226 001 India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110 025 India
- Department of Botany, University of Delhi, New Delhi, 110 007 India
| | - Vandana Jaiswal
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, UP 226 001 India
| | - Samir V. Sawant
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, UP 226 001 India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110 025 India
| | - Hemant Kumar Yadav
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, UP 226 001 India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110 025 India
| |
Collapse
|
14
|
Update of Genetic Linkage Map and QTL Analysis for Growth Traits in Eucommia ulmoides Oliver. FORESTS 2020. [DOI: 10.3390/f11030311] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Eucommia ulmoides (Tu-chung) is an economically and ecologically important tree species which has attracted worldwide attention due to its application in pharmacology, landscaping, wind sheltering and sand fixation. Molecular marker technologies can elucidate the genetic mechanism and substantially improve the breeding efficiency of E. ulmoides. The current research updated the original linkage map, and quantitative trait loci (QTL) analysis was performed on tree growth traits measured over 10 consecutive years in an E. ulmoides F1 population (“Xiaoye” × “Qinzhong No.1”). In total, 452 polymorphic markers were scored from 365 simple sequence repeat (SSR) primers, with an average of 1.24 polymorphic markers per primer combination. The integrated map was 1913.29 cM (centimorgan) long, covering 94.10% of the estimated genome and with an average marker density of 2.20 cM. A total of 869 markers were mapped into 19 major independent linkage groups. Growth-related traits measured over 10 consecutive years showed a significant correlation, and 89 hypothetical QTLs were forecasted and divided into 27 distinct loci. Three traits for tree height, ground diameter and crown diameter detected 25 QTLs (13 loci), 32 QTLs (17 loci) and 15 QTLs (10 loci), respectively. Based on BLASTX search results in the NCBI database, six candidate genes were obtained. It is important to explore the growth-related genetic mechanism and lay the foundation for the genetic improvement of E. ulmoides at the molecular level.
Collapse
|
15
|
Lu N, Zhang M, Xiao Y, Han D, Liu Y, Zhang Y, Yi F, Zhu T, Ma W, Fan E, Qu G, Wang J. Construction of a high-density genetic map and QTL mapping of leaf traits and plant growth in an interspecific F 1 population of Catalpa bungei × Catalpa duclouxii Dode. BMC PLANT BIOLOGY 2019; 19:596. [PMID: 31888555 PMCID: PMC6937828 DOI: 10.1186/s12870-019-2207-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 12/17/2019] [Indexed: 05/08/2023]
Abstract
BACKGROUND Catalpa bungei is an important tree species used for timber in China and widely cultivated for economic and ornamental purposes. A high-density linkage map of C. bungei would be an efficient tool not only for identifying key quantitative trait loci (QTLs) that affect important traits, such as plant growth and leaf traits, but also for other genetic studies. RESULTS Restriction site-associated DNA sequencing (RAD-seq) was used to identify molecular markers and construct a genetic map. Approximately 280.77 Gb of clean data were obtained after sequencing, and in total, 25,614,295 single nucleotide polymorphisms (SNPs) and 2,871,647 insertions-deletions (InDels) were initially identified in the genomes of 200 individuals of a C. bungei (7080) × Catalpa duclouxii (16-PJ-3) F1 population and their parents. Finally, 9072 SNP and 521 InDel markers that satisfied the requirements for constructing a genetic map were obtained. The integrated genetic map contained 9593 pleomorphic markers in 20 linkage groups and spanned 3151.63 cM, with an average distance between adjacent markers of 0.32 cM. Twenty QTLs for seven leaf traits and 13 QTLs for plant height at five successive time points were identified using our genetic map by inclusive composite interval mapping (ICIM). Q16-60 was identified as a QTL for five leaf traits, and three significant QTLs (Q9-1, Q18-66 and Q18-73) associated with plant growth were detected at least twice. Genome annotation suggested that a cyclin gene participates in leaf trait development, while the growth of C. bungei may be influenced by CDC48C and genes associated with phytohormone synthesis. CONCLUSIONS This is the first genetic map constructed in C. bungei and will be a useful tool for further genetic study, molecular marker-assisted breeding and genome assembly.
Collapse
Affiliation(s)
- Nan Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Miaomiao Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Yao Xiao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Donghua Han
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, 210037 Jiangsu People’s Republic of China
| | - Ying Liu
- College of Forestry, Northwest A&F University, Yangling, 712100 Shaanxi People’s Republic of China
| | - Yu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Fei Yi
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Tianqing Zhu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Wenjun Ma
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Erqin Fan
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, People’s Republic of China
| | - Guanzheng Qu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, People’s Republic of China
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| |
Collapse
|
16
|
Cai X, Magwanga RO, Xu Y, Zhou Z, Wang X, Hou Y, Wang Y, Zhang Y, Liu F, Wang K. Comparative transcriptome, physiological and biochemical analyses reveal response mechanism mediated by CBF4 and ICE2 in enhancing cold stress tolerance in Gossypium thurberi. AOB PLANTS 2019; 11:plz045. [PMID: 31777648 PMCID: PMC6863471 DOI: 10.1093/aobpla/plz045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 07/10/2019] [Indexed: 05/04/2023]
Abstract
Low temperature is one of the key environmental stresses that impair plant growth and significantly restricts the productivity and spatial distribution of crop plants. Gossypium thurberi, a wild diploid cotton species, has adapted to a wide range of temperatures and exhibits a better tolerance to chilling stress. Here, we compared phenotypes and physiochemical changes in G. thurberi under cold stress and found this species indeed showed better cold tolerance. Therefore, to understand the molecular mechanisms of the cold tolerance in G. thurberi, we compared transcription changes in leaves of G. thurberi under cold stress by high-throughput transcriptome sequencing. In total, 35 617 unigenes were identified in the whole-genome transcription profile, and 4226 differentially expressed genes (DEGs) were discovered in the leaves upon cold treatment. Gene Ontology (GO) classification analyses showed that the majority of DEGs belonged to categories of signal transduction, transcription factors (TFs) and carbohydrate transport and metabolism. The expression of several cold-responsive genes such as ICE1, CBF4, RAP2-7 and abscisic acid (ABA) biosynthesis genes involved in different signalling pathways were induced after G. thurberi seedlings were exposed to cold stress. Furthermore, cold sensitivity was increased in CBF4 and ICE2 virus-induced gene silencing (VIGS) plants, and high level of malondialdehyde (MDA) showed that the CBF4 and ICE2 silenced plants were under oxidative stress compared to their wild types, which relatively had higher levels of antioxidant enzyme activity, as evident by high levels of proline and superoxide dismutase (SOD) content. In conclusion, our findings reveal a new regulatory network of cold stress response in G. thurberi and broaden our understanding of the cold tolerance mechanism in cotton, which might accelerate functional genomics studies and genetic improvement for cold stress tolerance in cultivated cotton.
Collapse
Affiliation(s)
- Xiaoyan Cai
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Richard Odongo Magwanga
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, China
- School of Biological and Physical Sciences (SBPS), Jaramogi Oginga Odinga University of Science and Technology (JOOUST), Bondo, Kenya
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Xingxing Wang
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Yuqing Hou
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Yuhong Wang
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Yuanming Zhang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Fang Liu
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, China
| |
Collapse
|
17
|
Li P, Kirungu JN, Lu H, Magwanga RO, Lu P, Cai X, Zhou Z, Wang X, Hou Y, Wang Y, Xu Y, Peng R, Cai Y, Zhou Y, Wang K, Liu F. SSR-Linkage map of interspecific populations derived from Gossypium trilobum and Gossypium thurberi and determination of genes harbored within the segregating distortion regions. PLoS One 2018; 13:e0207271. [PMID: 30419064 PMCID: PMC6231669 DOI: 10.1371/journal.pone.0207271] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/29/2018] [Indexed: 12/17/2022] Open
Abstract
Wild cotton species have significant agronomic traits that can be introgressed into elite cultivated varieties. The use of a genetic map is important in exploring, identification and mining genes which carry significant traits. In this study, 188 F2mapping individuals were developed from Gossypium thurberi (female) and Gossypium trilobum (male), and were genotyped by using simple sequence repeat (SSR) markers. A total of 12,560 simple sequence repeat (SSR) markers, developed by Southwest University, thus coded SWU were screened out of which only 994 were found to be polymorphic, and 849 markers were linked in all the 13 chromosomes. The map had a length of 1,012.458 cM with an average marker distance of 1.193 cM. Segregation distortion regions (SDRs) were observed on Chr01, Chr02, Chr06, Chr07 Chr09, Chr10 and Chr11 with a large proportion of the SDR regions segregating towards the heterozygous allele. There was good syntenic block formation that revealed good collinearity between the genetic and physical map of G. raimondii, compared to the Dt_sub genome of the G. hirsutum and G. barbadense. A total of 2,496 genes were mined within the SSR related regions. The proteins encoding the mined genes within the SDR had varied physiochemical properties; their molecular weights ranged from 6.586 to 252.737 kDa, charge range of -39.5 to 52, grand hydropathy value (GRAVY) of -1.177 to 0.936 and isoelectric (pI) value of 4.087 to 12.206. The low GRAVY values detected showed that the proteins encoding these genes were hydrophilic in nature, a property common among the stress responsive genes. The RNA sequence analysis revealed more of the genes were highly upregulated in various stages of fiber development for instance; Gorai.002G241300 was highly up regulated at 5, 10, 20 and 25 day post anthesis (DPA). Validation through RT-qPCR further revealed that these genes mined within the SDR regions might be playing a significant role under fiber development stages, therefore we infer that Gorai.007G347600 (TFCA), Gorai.012G141600 (FOLB1), Gorai.006G024500 (NMD3), Gorai.002G229900 (LST8) and Gorai.002G235200 (NSA2) are significantly important in fiber development and in turn the quality, and further researches needed to be done to elucidate their exact roles in the fiber development process. The construction of the genetic map between the two wild species paves away for the mapping of quantitative trait loci (QTLs) since the average distance between the markers is small, and mining of genes on the SSR regions will provide an insight in identifying key genes that can be introgressed into the cultivated cotton cultivars.
Collapse
Affiliation(s)
- Pengcheng Li
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, China
- School of Life Science, Henan University/State Key Laboratory of Cotton Biology/Henan Key Laboratory of Plant Stress Biology, Kaifeng, Henan, China
| | - Joy Nyangasi Kirungu
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Hejun Lu
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Richard Odongo Magwanga
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, China
- School of Biological and Physical Sciences (SBPS), Jaramogi Oginga Odinga University of Science and Technology (JOOUST), Bondo- Kenya
| | - Pu Lu
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Xingxing Wang
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Yuqing Hou
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Yuhong Wang
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Renhai Peng
- Biological and Food Engineering, Anyang Institute of technology, Anyang, Henan, China
| | - Yingfan Cai
- School of Life Science, Henan University/State Key Laboratory of Cotton Biology/Henan Key Laboratory of Plant Stress Biology, Kaifeng, Henan, China
| | - Yun Zhou
- School of Life Science, Henan University/State Key Laboratory of Cotton Biology/Henan Key Laboratory of Plant Stress Biology, Kaifeng, Henan, China
- * E-mail: (YZ); (KW); (FL)
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, China
- * E-mail: (YZ); (KW); (FL)
| | - Fang Liu
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, China
- * E-mail: (YZ); (KW); (FL)
| |
Collapse
|
18
|
Li J, Zhang D, Ouyang K, Chen X. The complete chloroplast genome of the miracle tree Neolamarckia cadamba and its comparison in Rubiaceae family. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1496034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Affiliation(s)
- Jingjian Li
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, PR China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, PR China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, PR China
| | - Deng Zhang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, PR China
| | - Kunxi Ouyang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, PR China
| | - Xiaoyang Chen
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, PR China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, PR China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, PR China
| |
Collapse
|
19
|
Ditta A, Zhou Z, Cai X, Wang X, Okubazghi KW, Shehzad M, Xu Y, Hou Y, Sajid Iqbal M, Khan MKR, Wang K, Liu F. Assessment of Genetic Diversity, Population Structure, and Evolutionary Relationship of Uncharacterized Genes in a Novel Germplasm Collection of Diploid and Allotetraploid Gossypium Accessions Using EST and Genomic SSR Markers. Int J Mol Sci 2018; 19:E2401. [PMID: 30110970 PMCID: PMC6121227 DOI: 10.3390/ijms19082401] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 08/08/2018] [Accepted: 08/13/2018] [Indexed: 11/17/2022] Open
Abstract
This study evaluated the genetic diversity and population structures in a novel cotton germplasm collection comprising 132 diploids, including Glossypium klotzschianum and allotetraploid cotton accessions, including Glossypium barbadense, Glossypium darwinii, Glossypium tomentosum, Glossypium ekmanianum, and Glossypium stephensii, from Santa Cruz, Isabella, San Cristobal, Hawaiian, Dominican Republic, and Wake Atoll islands. A total of 111 expressed sequence tag (EST) and genomic simple sequence repeat (gSSR) markers produced 382 polymorphic loci with an average of 3.44 polymorphic alleles per SSR marker. Polymorphism information content values counted 0.08 to 0.82 with an average of 0.56. Analysis of a genetic distance matrix revealed values of 0.003 to 0.53 with an average of 0.33 in the wild cotton collection. Phylogenetic analysis supported the subgroups identified by STRUCTURE and corresponds well with the results of principal coordinate analysis with a cumulative variation of 45.65%. A total of 123 unique alleles were observed among all accessions and 31 identified only in G. ekmanianum. Analysis of molecular variance revealed highly significant variation between the six groups identified by structure analysis with 49% of the total variation and 51% of the variation was due to diversity within the groups. The highest genetic differentiation among tetraploid populations was observed between accessions from the Hawaiian and Santa Cruz regions with a pairwise FST of 0.752 (p < 0.001). DUF819 containing an uncharacterized gene named yjcL linked to genomic markers has been found to be highly related to tryptophan-aspartic acid (W-D) repeats in a superfamily of genes. The RNA sequence expression data of the yjcL-linked gene Gh_A09G2500 was found to be upregulated under drought and salt stress conditions. The existence of genetic diversity, characterization of genes and variation in novel germplasm collection will be a landmark addition to the genetic study of cotton germplasm.
Collapse
Affiliation(s)
- Allah Ditta
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
- Nuclear Institute for Agriculture and Biology (NIAB), Jhang Road, Faisalabad 38000, Punjab, Pakistan.
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
| | - Xingxing Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
| | - Kiflom Weldu Okubazghi
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
- Hamelmalo Agricultural College, P.O. Box 397, Keren, Eritrea.
| | - Muhammad Shehzad
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
| | - Yuqing Hou
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
| | - Muhammad Sajid Iqbal
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
| | - Muhammad Kashif Riaz Khan
- Nuclear Institute for Agriculture and Biology (NIAB), Jhang Road, Faisalabad 38000, Punjab, Pakistan.
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
| | - Fang Liu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
| |
Collapse
|
20
|
Magwanga RO, Lu P, Kirungu JN, Diouf L, Dong Q, Hu Y, Cai X, Xu Y, Hou Y, Zhou Z, Wang X, Wang K, Liu F. GBS Mapping and Analysis of Genes Conserved between Gossypium tomentosum and Gossypium hirsutum Cotton Cultivars that Respond to Drought Stress at the Seedling Stage of the BC₂F₂ Generation. Int J Mol Sci 2018; 19:E1614. [PMID: 29848989 PMCID: PMC6032168 DOI: 10.3390/ijms19061614] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/21/2018] [Accepted: 05/28/2018] [Indexed: 12/13/2022] Open
Abstract
Cotton production is on the decline due to ever-changing environmental conditions. Drought and salinity stress contribute to over 30% of total loss in cotton production, the situation has worsened more due to the narrow genetic base of the cultivated upland cotton. The genetic diversity of upland cotton has been eroded over the years due to intense selection and inbreeding. To break the bottleneck, the wild cotton progenitors offer unique traits which can be introgressed into the cultivated cotton, thereby improving their performance. In this research, we developed a BC₂F₂ population between wild male parent, G. tomentosum as the donor, known for its high tolerance to drought and the elite female parent, G. hirsutum as the recurrent parent, which is high yielding but sensitive to drought stress. The population was genotyped through the genotyping by sequencing (GBS) method, in which 10,888 single-nucleotide polymorphism (SNP) s were generated and used to construct a genetic map. The map spanned 4191.3 cM, with average marker distance of 0.3849 cM. The map size of the two sub genomes had a narrow range, 2149 cM and 2042.3 cM for At and Dt_sub genomes respectively. A total of 66,434 genes were mined, with 32,032 (48.2%) and 34,402 (51.8%) genes being obtained within the At and Dt_sub genomes respectively. Pkinase (PF00069) was found to be the dominant domain, with 1069 genes. Analysis of the main sub family, serine threonine protein kinases through gene ontology (GO), cis element and miRNA targets analysis revealed that most of the genes were involved in various functions aimed at enhancing abiotic stress tolerance. Further analysis of the RNA sequence data and qRT-PCR validation revealed 16 putative genes, which were highly up regulated under drought stress condition, and were found to be targeted by ghr-miR169a and ghr-miR164, previously associated with NAC(NAM, ATAF1/2 and CUC2) and myeloblastosis (MYB), the top rank drought stress tolerance genes. These genes can be exploited further to aid in development of more drought tolerant cotton genotypes.
Collapse
Affiliation(s)
- Richard Odongo Magwanga
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
- School of Biological and Physical Sciences (SBPS), Main Campus, Jaramogi Oginga Odinga University of Science and Technology (JOOUST), Main Campus, P.O. Box 210-40601 Bondo, Kenya.
| | - Pu Lu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Joy Nyangasi Kirungu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Latyr Diouf
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Qi Dong
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Yangguang Hu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Yuqing Hou
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Xingxing Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Fang Liu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| |
Collapse
|