1
|
Dossa K, Morel A, Houngbo ME, Mota AZ, Malédon E, Irep JL, Diman JL, Mournet P, Causse S, Van KN, Cornet D, Chair H. Genome-wide association studies reveal novel loci controlling tuber flesh color and oxidative browning in Dioscorea alata. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:4895-4906. [PMID: 37209230 DOI: 10.1002/jsfa.12721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 03/28/2023] [Accepted: 05/20/2023] [Indexed: 05/22/2023]
Abstract
BACKGROUND Consumers' preferences for food crops are guided by quality attributes. This study aimed at deciphering the genetic basis of quality traits, especially tuber flesh color (FC) and oxidative browning (OB) in Dioscorea alata, based on the genome-wide association studies (GWAS) approach. The D. alata panel was planted at two locations in Guadeloupe. At harvest, the FC was scored visually as white, cream, or purple on longitudinally sliced mature tubers. The OB was scored visually as the presence or absence of browning after 15 min of exposure of the sliced samples to ambient air. RESULTS Phenotypic characterization for FC and OB of a diverse panel of D. alata genotypes highlighted significant variation within the panel and across two locations. The genotypes within the panel displayed a weak structure and could be classified into three subpopulations. GWAS identified 14 and 4 significant associations for tuber FC and OB, respectively, with phenotypic variance, explained values ranging from 7.18% to 18.04%. Allele segregation analysis at the significantly associated loci highlighted the favorable alleles for the desired traits, i.e., white FC and no OB. A total of 24 putative candidate genes were identified around the significant signals. A comparative analysis with previously reported quantitative trait loci indicated that numerous genomic regions control these traits in D. alata. CONCLUSION Our study provides important insights into the genetic control of tuber FC and OB in D. alata. The major and stable loci can be further utilized to improve selection in breeding programs for developing new cultivars with enhanced tuber quality. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
Collapse
Affiliation(s)
- Komivi Dossa
- CIRAD, UMR AGAP Institut, Petit Bourg, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Angélique Morel
- CIRAD, UMR AGAP Institut, Petit Bourg, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Mahugnon Ezékiel Houngbo
- CIRAD, UMR AGAP Institut, Petit Bourg, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, Montpellier, France
| | - Ana Zotta Mota
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, Montpellier, France
| | | | - Jean-Luc Irep
- UR1321 ASTRO Agrosystèmes tropicaux, INRAE, Petit-Bourg (Guadeloupe), Paris, France
| | - Jean-Louis Diman
- UR1321 ASTRO Agrosystèmes tropicaux, INRAE, Petit-Bourg (Guadeloupe), Paris, France
| | - Pierre Mournet
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, Montpellier, France
| | - Sandrine Causse
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, Montpellier, France
| | | | - Denis Cornet
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, Montpellier, France
| | - Hâna Chair
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, Montpellier, France
| |
Collapse
|
2
|
Rehman A, Tian C, He S, Li H, Lu S, Du X, Peng Z. Transcriptome dynamics of Gossypium purpurascens in response to abiotic stresses by Iso-seq and RNA-seq data. Sci Data 2024; 11:477. [PMID: 38724643 PMCID: PMC11081948 DOI: 10.1038/s41597-024-03334-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/30/2024] [Indexed: 05/12/2024] Open
Abstract
Gossypium purpurascens is a member of the Malvaceae family, holds immense economic significance as a fiber crop worldwide. Abiotic stresses harm cotton crops, reduce yields, and cause economic losses. Generating high-quality reference genomes and large-scale transcriptomic datasets across diverse conditions can offer valuable insights into identifying preferred agronomic traits for crop breeding. The present research used leaf tissues to conduct PacBio Iso-seq and RNA-seq analysis. We carried out an in-depth analysis of DEGs using both correlations with cluster analysis and principal component analysis. Additionally, the study also involved the identification of both lncRNAs and CDS. We have prepared RNA-seq libraries from 75 RNA samples to study the effects of drought, salinity, alkali, and saline-alkali stress, as well as control conditions. A total of 454.06 Gigabytes of transcriptome data were effectively validated through the identification of differentially expressed genes and KEGG and GO analysis. Overwhelmingly, gene expression profiles and full-length transcripts from cotton tissues will aid in understanding the genetic mechanism of abiotic stress tolerance in G. purpurascens.
Collapse
Affiliation(s)
- Abdul Rehman
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Chunyan Tian
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Shoupu He
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, Henan, 455000, China
| | - Hongge Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, Henan, 455000, China
| | - Shuai Lu
- National Supercomputing Center in Zhengzhou, Zhengzhou University, Zhengzhou, 450001, China
| | - Xiongming Du
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, Henan, 455000, China.
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, 572024, China.
| | - Zhen Peng
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, Henan, 455000, China.
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, 572024, China.
| |
Collapse
|
3
|
Nazir MF, Wang J, Chen B, Umer MJ, He S, Pan Z, Hu D, Song M, Du X. Multistage temporal transcriptomic atlas unveils major contributor to reproductive phase in upland cotton. PHYSIOLOGIA PLANTARUM 2024; 176:e14382. [PMID: 38859666 DOI: 10.1111/ppl.14382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 05/11/2024] [Indexed: 06/12/2024]
Abstract
Flowering is a major developmental transition in plants, but asynchronous flowering hinders the utilization of wild cotton relatives in breeding programs. We performed comparative transcriptomic profiling of early- and late-flowering Gossypium hirsutum genotypes to elucidate genetic factors influencing reproductive timing. Shoot apices were sampled from the photoperiod-sensitive landrace G. hirsutum purpurascens (GhP) and early-maturing variety ZhongMianSuo (ZMS) at five time points following the emergence of sympodial nodes. RNA-sequencing revealed extensive transcriptional differences during floral transition. Numerous flowering-associated genes exhibited genotype-specific expression, including FLOWERING LOCUS T (FT) homologs upregulated in ZMS. FT-interacting factors like SOC1 and CO-like also showed higher expression in ZMS, implicating florigen pathways in early flowering. Additionally, circadian clock and light signalling components were misregulated between varieties, suggesting altered photoperiod responses in GhP. Weighted co-expression network analysis specifically linked a module enriched for circadian-related genes to GhP's late flowering. Through an integrated transcriptome analysis, we defined a regulatory landscape of reproductive phase change in cotton. Differentially expressed genes related to photoperiod, circadian clock, and light signalling likely contribute to delayed flowering in wild cottons. Characterization of upstream flowering regulators will enable modifying photoperiod sensitivity and expand germplasm use for cotton improvement. This study provides candidate targets for elucidating interactive mechanisms that control cotton flowering time across diverse genotypes.
Collapse
Affiliation(s)
- Mian Faisal Nazir
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, China
- Jiangxi Provincial Key Laboratory of ex situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, China
| | - Jingjing Wang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, China
| | - Baojun Chen
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, China
| | - Muhammad Jawad Umer
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, China
| | - Shoupu He
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, China
| | - Zhaoe Pan
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, China
| | - Daowu Hu
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, China
| | - Meizhen Song
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, China
| | - Xiongming Du
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, China
| |
Collapse
|
4
|
Cheng Y, Huang C, Hu Y, Jin S, Zhang X, Si Z, Zhao T, Chen J, Fang L, Dai F, Yang W, Wang P, Mei G, Guan X, Zhang T. Gossypium purpurascens genome provides insight into the origin and domestication of upland cotton. J Adv Res 2024; 56:15-29. [PMID: 36966917 PMCID: PMC10834806 DOI: 10.1016/j.jare.2023.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/02/2023] [Accepted: 03/17/2023] [Indexed: 03/29/2023] Open
Abstract
INTRODUCTION Allotetraploid upland cotton (Gossypium hirsutum L.) is native to the Mesoamerican and Caribbean regions, had been improved in the southern United States by the mid-eighteenth century, was then dispersed worldwide. However, a Hainan Island Native Cotton (HIC) has long been grown extensively on Hainan Island, China. OBJECTIVES Explore HIC's evolutionary relationship and genomic diversity with other tetraploid cottons, its origin and whether it was used for YAZHOUBU (Yazhou cloth, World Intangible Cultural Heritage) weaving, and the role of structural variations (SVs) in upland cotton domestication. METHODS We assembled a high-quality genome of one HIC plant. We performed phylogenetic analysis, divergence time estimation, principal component analysis and population differentiation estimation using cotton assemblies and/or resequencing data. SVs were detected by whole-genome comparison. A F2 population was used for linkage analysis and to study effects of SVs. Buoyancy and salt water tolerance tests for seeds were conducted. RESULTS We found that the HIC belongs to G. purpurascens. G. purpurascens is best classified as a primitive race of G. hirsutum. The potential for long range transoceanic dispersal of G. purpurascens seeds was proved. A set of SVs, selective sweep regions between G. hirsutum races and cultivars, and quantitative trait loci (QTLs) of eleven agronomic traits were obtained. SVs, especially large-scale SVs, were found to have important effects on cotton domestication and improvement. Of them, eight large-scale inversions strongly associated with yield and fiber quality have probably undergone artificial selection in domestication. CONCLUSION G. purpurascens including HIC is a primitive race of G. hirsutum, probably disperse to Hainan from Central America by floating on ocean currents, may have been partly domesticated, planted and was likely used for YAZHOUBU weaving in Hainan much earlier than the Pre-Columbian period. SV plays an important role in cotton domestication and improvement.
Collapse
Affiliation(s)
- Yu Cheng
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Chujun Huang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yan Hu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Shangkun Jin
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xuemei Zhang
- Annoroad Gene Technology (Beijing) Co., Ltd., Beijing 100176, China
| | - Zhanfeng Si
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Ting Zhao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Jinwen Chen
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Lei Fang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Fan Dai
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Weifei Yang
- Annoroad Gene Technology (Beijing) Co., Ltd., Beijing 100176, China
| | - Peizheng Wang
- Hainan Tropical Ocean University, Sanya 572022, China
| | - Gaofu Mei
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xueying Guan
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Tianzhen Zhang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China.
| |
Collapse
|
5
|
Nazir MF, Chen B, Umer MJ, Sarfraz Z, Peng Z, He S, Iqbal MS, Wang J, Li H, Pan Z, Hu D, Song M, Du X. Transcriptomic analysis reveals the beneficial effects of salt priming on enhancing defense responses in upland cotton under successive salt stress. PHYSIOLOGIA PLANTARUM 2023; 175:e14074. [PMID: 38148226 DOI: 10.1111/ppl.14074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/11/2023] [Accepted: 10/24/2023] [Indexed: 12/28/2023]
Abstract
Priming-mediated stress tolerance in plants stimulates defense mechanisms and enables plants to cope with future stresses. Seed priming has been proven effective for tolerance against abiotic stresses; however, underlying genetic mechanisms are still unknown. We aimed to assess upland cotton genotypes and their transcriptional behaviors under salt priming and successive induced salt stress. We pre-selected 16 genotypes based on previous studies and performed morpho-physiological characterization, from which we selected three genotypes, representing different tolerance levels, for transcriptomic analysis. We subjected these genotypes to four different treatments: salt priming (P0), salt priming with salinity dose at 3-true-leaf stage (PD), salinity dose at 3-true-leaf stage without salt priming (0D), and control (CK). Although the three genotypes displayed distinct expression patterns, we identified common differentially expressed genes (DEGs) under PD enriched in pathways related to transferase activity, terpene synthase activity, lipid biosynthesis, and regulation of acquired resistance, indicating the beneficial role of salt priming in enhancing salt stress resistance. Moreover, the number of unique DEGs associated with G. hirsutum purpurascens was significantly higher compared to other genotypes. Coexpression network analysis identified 16 hub genes involved in cell wall biogenesis, glucan metabolic processes, and ribosomal RNA binding. Functional characterization of XTH6 (XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE) using virus-induced gene silencing revealed that suppressing its expression improves plant growth under salt stress. Overall, findings provide insights into the regulation of candidate genes in response to salt stress and the beneficial effects of salt priming on enhancing defense responses in upland cotton.
Collapse
Affiliation(s)
- Mian Faisal Nazir
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), China
| | - Baojun Chen
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), China
| | - Muhammad Jawad Umer
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), China
| | - Zareen Sarfraz
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), China
| | - Zhen Peng
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), China
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
| | - Shoupu He
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), China
| | - Muhammad Shahid Iqbal
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), China
| | - Jingjing Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), China
| | - Hongge Li
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), China
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
| | - Zhaoe Pan
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), China
| | - Daowu Hu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), China
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
| | - Meizhen Song
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), China
| | - Xiongming Du
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), China
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
| |
Collapse
|
6
|
Peng Z, Rehman A, Li X, Jiang X, Tian C, Wang X, Li H, Wang Z, He S, Du X. Comprehensive Evaluation and Transcriptome Analysis Reveal the Salt Tolerance Mechanism in Semi-Wild Cotton ( Gossypium purpurascens). Int J Mol Sci 2023; 24:12853. [PMID: 37629034 PMCID: PMC10454576 DOI: 10.3390/ijms241612853] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/03/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Elevated salinity significantly threatens cotton growth, particularly during the germination and seedling stages. The utilization of primitive species of Gossypium hirsutum, specifically Gossypium purpurascens, has the potential to facilitate the restoration of genetic diversity that has been depleted due to selective breeding in modern cultivars. This investigation evaluated 45 G. purpurascens varieties and a salt-tolerant cotton variety based on 34 morphological, physiological, and biochemical indicators and comprehensive salt tolerance index values. This study effectively identified a total of 19 salt-tolerant and two salt-resistant varieties. Furthermore, transcriptome sequencing of a salt-tolerant genotype (Nayanmian-2; NY2) and a salt-sensitive genotype (Sanshagaopao-2; GP2) revealed 2776, 6680, 4660, and 4174 differentially expressed genes (DEGs) under 0.5, 3, 12, and 24 h of salt stress. Gene ontology enrichment analysis indicated that the DEGs exhibited significant enrichment in biological processes like metabolic (GO:0008152) and cellular (GO:0009987) processes. MAPK signaling, plant-pathogen interaction, starch and sucrose metabolism, plant hormone signaling, photosynthesis, and fatty acid metabolism were identified as key KEGG pathways involved in salinity stress. Among the DEGs, including NAC, MYB, WRKY, ERF, bHLH, and bZIP, transcription factors, receptor-like kinases, and carbohydrate-active enzymes were crucial in salinity tolerance. Weighted gene co-expression network analysis (WGCNA) unveiled associations of salt-tolerant genotypes with flavonoid metabolism, carbon metabolism, and MAPK signaling pathways. Identifying nine hub genes (MYB4, MYB105, MYB36, bZIP19, bZIP43, FRS2 SMARCAL1, BBX21, F-box) across various intervals offered insights into the transcriptional regulation mechanism of salt tolerance in G. purpurascens. This study lays the groundwork for understanding the important pathways and gene networks in response to salt stress, thereby providing a foundation for enhancing salt tolerance in upland cotton.
Collapse
Affiliation(s)
- Zhen Peng
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.P.); (A.R.); (X.L.); (X.J.); (C.T.); (X.W.); (H.L.)
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China;
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572025, China
| | - Abdul Rehman
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.P.); (A.R.); (X.L.); (X.J.); (C.T.); (X.W.); (H.L.)
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China;
| | - Xiawen Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.P.); (A.R.); (X.L.); (X.J.); (C.T.); (X.W.); (H.L.)
| | - Xuran Jiang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.P.); (A.R.); (X.L.); (X.J.); (C.T.); (X.W.); (H.L.)
| | - Chunyan Tian
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.P.); (A.R.); (X.L.); (X.J.); (C.T.); (X.W.); (H.L.)
| | - Xiaoyang Wang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.P.); (A.R.); (X.L.); (X.J.); (C.T.); (X.W.); (H.L.)
| | - Hongge Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.P.); (A.R.); (X.L.); (X.J.); (C.T.); (X.W.); (H.L.)
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China;
| | - Zhenzhen Wang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China;
| | - Shoupu He
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.P.); (A.R.); (X.L.); (X.J.); (C.T.); (X.W.); (H.L.)
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China;
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572025, China
| | - Xiongming Du
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.P.); (A.R.); (X.L.); (X.J.); (C.T.); (X.W.); (H.L.)
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China;
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572025, China
| |
Collapse
|
7
|
Yang L, Chen Y, Wang M, Hou H, Li S, Guan L, Yang H, Wang W, Hong L. Metabolomic and transcriptomic analyses reveal the effects of grafting on blood orange quality. FRONTIERS IN PLANT SCIENCE 2023; 14:1169220. [PMID: 37360739 PMCID: PMC10286243 DOI: 10.3389/fpls.2023.1169220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 05/02/2023] [Indexed: 06/28/2023]
Abstract
Introduction Blood orange (Citrus sinensis L.) is a valuable source of nutrition because it is enriched in anthocyanins and has high organoleptic properties. Grafting is commonly used in citriculture and has crucial effects on various phenotypes of the blood orange, including its coloration, phenology, and biotic and abiotic resistance. Still, the underlying genetics and regulatory mechanisms are largely unexplored. Methods In this study, we investigated the phenotypic, metabolomic, and transcriptomic profiles at eight developmental stages of the lido blood orange cultivar (Citrus sinensis L. Osbeck cv. Lido) grafted onto two rootstocks. Results and discussion The Trifoliate orange rootstock provided the best fruit quality and flesh color for Lido blood orange. Comparative metabolomics suggested significant differences in accumulation patterns of metabolites and we identified 295 differentially accumulated metabolites. The major contributors were flavonoids, phenolic acids, lignans and coumarins, and terpenoids. Moreover, transcriptome profiling resulted in the identification of 4179 differentially expressed genes (DEGs), and 54 DEGs were associated with flavonoids and anthocyanins. Weighted gene co-expression network analysis identified major genes associated to 16 anthocyanins. Furthermore, seven transcription factors (C2H2, GANT, MYB-related, AP2/ERF, NAC, bZIP, and MYB) and five genes associated with anthocyanin synthesis pathway (CHS, F3H, UFGT, and ANS) were identified as key modulators of the anthocyanin content in lido blood orange. Overall, our results revealed the impact of rootstock on the global transcriptome and metabolome in relation to fruit quality in lido blood orange. The identified key genes and metabolites can be further utilized for the quality improvement of blood orange varieties.
Collapse
Affiliation(s)
- Lei Yang
- Fruit Tree Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing, China
| | - Yang Chen
- Biotechnology Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing, China
| | - Min Wang
- Fruit Tree Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing, China
| | - Huifang Hou
- Fruit Tree Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing, China
| | - Shuang Li
- Fruit Tree Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing, China
| | - Ling Guan
- Biotechnology Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing, China
| | - Haijian Yang
- Fruit Tree Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing, China
| | - Wu Wang
- Fruit Tree Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing, China
| | - Lin Hong
- Fruit Tree Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing, China
| |
Collapse
|
8
|
Zhai R, Huang A, Mo R, Zou C, Wei X, Yang M, Tan H, Huang K, Qin J. SNP-based bulk segregant analysis revealed disease resistance QTLs associated with northern corn leaf blight in maize. Front Genet 2022; 13:1038948. [PMID: 36506330 PMCID: PMC9732028 DOI: 10.3389/fgene.2022.1038948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/31/2022] [Indexed: 11/27/2022] Open
Abstract
Maize (Zea mays L.) is the most important food security crop worldwide. Northern corn leaf blight (NCLB), caused by Exserohilum turcicum, severely reduces production causing millions of dollars in losses worldwide. Therefore, this study aimed to identify significant QTLs associated with NCLB by utilizing next-generation sequencing-based bulked-segregant analysis (BSA). Parental lines GML71 (resistant) and Gui A10341 (susceptible) were used to develop segregating population F2. Two bulks with 30 plants each were further selected from the segregating population for sequencing along with the parental lines. High throughput sequencing data was used for BSA. We identified 10 QTLs on Chr 1, Chr 2, Chr 3, and Chr 5 with 265 non-synonymous SNPs. Moreover, based on annotation information, we identified 27 candidate genes in the QTL regions. The candidate genes associated with disease resistance include AATP1, At4g24790, STICHEL-like 2, BI O 3-BIO1, ZAR1, SECA2, ABCG25, LECRK54, MKK7, MKK9, RLK902, and DEAD-box ATP-dependent RNA helicase. The annotation information suggested their involvement in disease resistance-related pathways, including protein phosphorylation, cytoplasmic vesicle, protein serine/threonine kinase activity, and ATP binding pathways. Our study provides a substantial addition to the available information regarding QTLs associated with NCLB, and further functional verification of identified candidate genes can broaden the scope of understanding the NCLB resistance mechanism in maize.
Collapse
Affiliation(s)
- Ruining Zhai
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Aihua Huang
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Runxiu Mo
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Chenglin Zou
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Xinxing Wei
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Meng Yang
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Hua Tan
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Kaijian Huang
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China,*Correspondence: Kaijian Huang, ; Jie Qin,
| | - Jie Qin
- Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China,*Correspondence: Kaijian Huang, ; Jie Qin,
| |
Collapse
|
9
|
Kushanov FN, Komilov DJ, Turaev OS, Ernazarova DK, Amanboyeva RS, Gapparov BM, Yu JZ. Genetic Analysis of Mutagenesis That Induces the Photoperiod Insensitivity of Wild Cotton Gossypium hirsutum Subsp. purpurascens. PLANTS (BASEL, SWITZERLAND) 2022; 11:3012. [PMID: 36432741 PMCID: PMC9698681 DOI: 10.3390/plants11223012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/22/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
Cotton genus Gossypium L., especially its wild species, is rich in genetic diversity. However, this valuable genetic resource is barely used in cotton breeding programs. In part, due to photoperiod sensitivities, the genetic diversity of Gossypium remains largely untapped. Herein, we present a genetic analysis of morphological, cytological, and genomic changes from radiation-mediated mutagenesis that induced plant photoperiod insensitivity in the wild cotton of Gossypium hirsutum. Several morphological and agronomical traits were found to be highly inheritable using the progeny between the wild-type G. hirsutum subsp. purpurascens (El-Salvador) and its mutant line (Kupaysin). An analysis of pollen mother cells (PMCs) revealed quadrivalents that had an open ring shape and an adjoining type of divergence of chromosomes from translocation complexes. Using 336 SSR markers and 157 F2 progenies that were grown with parental genotypes and F1 hybrids in long day and short night conditions, five quantitative trait loci (QTLs) associated with cotton flowering were located on chromosomes At-05, At-11, and Dt-07. Nineteen candidate genes related to the flowering traits were suggested through molecular and in silico analysis. The DNA markers associated with the candidate genes, upon future functional analysis, would provide useful tools in marker-assisted selection (MAS) in cotton breeding programs for early flowering and maturity.
Collapse
Affiliation(s)
- Fakhriddin N. Kushanov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Qibray QFY, Yuqori-Yuz, Qibray District, Tashkent 111226, Uzbekistan
- Department of Biology, National University of Uzbekistan, University Street-4, Olmazor District, Tashkent 100174, Uzbekistan
- Department of Biotechnology, Namangan State University, Uychi Street-316, Namangan 160100, Uzbekistan
| | - Doniyor J. Komilov
- Department of Biotechnology, Namangan State University, Uychi Street-316, Namangan 160100, Uzbekistan
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, University Street-2, Qibray District, Tashkent 111215, Uzbekistan
| | - Ozod S. Turaev
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Qibray QFY, Yuqori-Yuz, Qibray District, Tashkent 111226, Uzbekistan
- Department of Biology, National University of Uzbekistan, University Street-4, Olmazor District, Tashkent 100174, Uzbekistan
| | - Dilrabo K. Ernazarova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Qibray QFY, Yuqori-Yuz, Qibray District, Tashkent 111226, Uzbekistan
- Department of Biology, National University of Uzbekistan, University Street-4, Olmazor District, Tashkent 100174, Uzbekistan
| | - Roza S. Amanboyeva
- Department of Biology, National University of Uzbekistan, University Street-4, Olmazor District, Tashkent 100174, Uzbekistan
- Faculty of Natural Sciences, Gulistan State University, 4th Microregion, Gulistan 120100, Uzbekistan
| | - Bunyod M. Gapparov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Qibray QFY, Yuqori-Yuz, Qibray District, Tashkent 111226, Uzbekistan
| | - John Z. Yu
- United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, TX 77845, USA
| |
Collapse
|
10
|
Yasir M, Kanwal HH, Hussain Q, Riaz MW, Sajjad M, Rong J, Jiang Y. Status and prospects of genome-wide association studies in cotton. FRONTIERS IN PLANT SCIENCE 2022; 13:1019347. [PMID: 36330239 PMCID: PMC9623101 DOI: 10.3389/fpls.2022.1019347] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
Over the last two decades, the use of high-density SNP arrays and DNA sequencing have allowed scientists to uncover the majority of the genotypic space for various crops, including cotton. Genome-wide association study (GWAS) links the dots between a phenotype and its underlying genetics across the genomes of populations. It was first developed and applied in the field of human disease genetics. Many areas of crop research have incorporated GWAS in plants and considerable literature has been published in the recent decade. Here we will provide a comprehensive review of GWAS studies in cotton crop, which includes case studies on biotic resistance, abiotic tolerance, fiber yield and quality traits, current status, prospects, bottlenecks of GWAS and finally, thought-provoking question. This review will serve as a catalog of GWAS in cotton and suggest new frontiers of the cotton crop to be studied with this important tool.
Collapse
Affiliation(s)
- Muhammad Yasir
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, China
| | - Hafiza Hamrah Kanwal
- School of Computer Science, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Quaid Hussain
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Muhammad Waheed Riaz
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Muhammad Sajjad
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Junkang Rong
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, China
| | - Yurong Jiang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, China
| |
Collapse
|
11
|
Genetic diversity and population structure of wild and cultivated Crotalaria species based on genotyping-by-sequencing. PLoS One 2022; 17:e0272955. [PMID: 36048841 PMCID: PMC9436042 DOI: 10.1371/journal.pone.0272955] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/28/2022] [Indexed: 11/19/2022] Open
Abstract
Crotalaria is a plant genus that is found all over the world, with over 700 species of herbs and shrubs. The species are potential alternative food and industrial crops due to their adaptability to different environments. Currently, information on the genetic diversity and population structure of these species is scanty. Genotyping-by-sequencing (GBS) is a cost-effective high-throughput technique in diversity evaluation of plant species that have not been fully sequenced. In the current study, de novo GBS was used to characterize 80 Crotalaria accessions from five geographical regions in Kenya. A total of 9820 single nucleotide polymorphism (SNP) markers were obtained after thinning and filtering, which were then used for the analysis of genetic diversity and population structure in Crotalaria. The proportion of SNPs with a minor allele frequency (maf) > = 0.05 was 45.08%, while the Guanine-Cytosine (GC) content was 0.45, from an average sequence depth of 455,909 reads per base. The transition vs transversion ratio was 1.81 and Heterozygosity (He) ranged between 0.01–0.07 in all the sites and 0.04 to 0.52 in the segregating sites. The mean Tajima’s D value for the population was -0.094, suggesting an excess of rare alleles. The fixation index (Fst) between the different populations based on the Wright Fst (1943) ranged from 0.0119 to 0.066 for the Eastern-Western and Nairobi-Western populations. Model based techniques of population structure analysis including structure, k-means and cross-entropy depicted eight clusters in the study accessions. Non-model based techniques especially DAPC depicted poor population stratification. Correspondence Analysis (CA), Principal coordinate analyses (PCoA) and phylogenetic analysis identified a moderate level of population stratification. Results from this study will help conservationists and breeders understand the genetic diversity of Crotalaria. The study also provides valuable information for genetic improvement of domesticated species.
Collapse
|
12
|
Lu L, Cao H, Li H, Zhang H, Li S, Wang J. Diversity and profiles of volatile compounds in twenty-five peppermint genotypes grown in China. INTERNATIONAL JOURNAL OF FOOD PROPERTIES 2022. [DOI: 10.1080/10942912.2022.2082465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Lin Lu
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Hua Cao
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Han Li
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Hao Zhang
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Shenchong Li
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Jihua Wang
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| |
Collapse
|
13
|
Insights into the Major Metabolites Involved in the Underground Floral Differentiation of Erythronium japonicum. BIOMED RESEARCH INTERNATIONAL 2022; 2022:7431151. [PMID: 35601148 PMCID: PMC9122723 DOI: 10.1155/2022/7431151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/30/2022] [Indexed: 11/17/2022]
Abstract
Background. Erythronium japonicum Decne (Liliaceae) is an early spring ephemeral with an underground initial floral differentiation stage. The flowering mechanism is crucial in ornamental plants due to the associated economic value. Therefore, this study is aimed at exploring the metabolic landscape during floral differentiation, including flower primordium, perianth, stamen, and the pistil differentiation period, in E. japonicum coupled with a conjoint analysis of the metabolome and transcriptome. Using ultraperformance liquid chromatography-tandem mass spectrometry, we identified 586 metabolites from 13 major metabolite classes. Comparative metabolomics between different floral developmental stages revealed several abundant metabolites during the respective phases. Upaccumulation of p-coumaroylputrescine, scopoletin, isorhoifolin, cosmosiin, genistin, and LysoPC 15 : 0 emphasized the significance of these compounds during flower development. Furthermore, previously identified DEGs, viz., EARLY FLOWERING 3, Flowering locus K, PHD finger-containing protein, and zinc finger SWIM domain-containing protein for floral differentiation, depicted a high correlation with lipid, flavonoid, and phenolics accumulation during floral developmental stages. Conclusions. Together, the results improve our interpretation of the underground floral development in E. japonicum.
Collapse
|
14
|
Shi R, Xiong B, He S, Liu C, Ben-Asher J, Horowitz AR, Wang S, He X. Comparative metabolic profiling of root, leaf, fruit, and stem tissues of Panax notoginseng. INTERNATIONAL JOURNAL OF FOOD PROPERTIES 2022. [DOI: 10.1080/10942912.2022.2071294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Rui Shi
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Bingjie Xiong
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Shu He
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Can Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Jiftah Ben-Asher
- French Associates Institute for Agriculture and Biotechnology of Dryland, the Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Israel
| | - Abraham Rami Horowitz
- French Associates Institute for Agriculture and Biotechnology of Dryland, the Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Israel
| | - Shu Wang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Xiahong He
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| |
Collapse
|
15
|
Yuan F, Lan X. Sequencing the organelle genomes of Bougainvillea spectabilis and Mirabilis jalapa (Nyctaginaceae). BMC Genom Data 2022; 23:28. [PMID: 35418016 PMCID: PMC9008926 DOI: 10.1186/s12863-022-01042-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 02/08/2022] [Indexed: 11/26/2022] Open
Abstract
Objectives Mirabilis jalapa L. and Bougainvillea spectabilis are two Mirabilis species known for their ornamental and pharmaceutical values. The organelle genomes are highly conserved with a rapid evolution rate making them suitable for evolutionary studies. Therefore, mitochondrial and chloroplast genomes of B. spectabilis and M. jalapa were sequenced to understand their evolutionary relationship with other angiosperms. Data description Here, we report the complete mitochondrial genomes of B. spectabilis and M. jalapa (343,746 bp and 267,334 bp, respectively) and chloroplast genomes of B. spectabilis (154,520 bp) and M. jalapa (154,532 bp) obtained from Illumina NovaSeq. The mitochondrial genomes of B. spectabilis and M. jalapa consisted of 70 and 72 genes, respectively. Likewise, the chloroplast genomes of B. spectabilis and M. jalapa contained 131 and 132 genes, respectively. The generated genomic data will be useful for molecular characterization and evolutionary studies.
Collapse
Affiliation(s)
- Fang Yuan
- Tibetan Collaborative Innovation Center of Agricultural and Animal Husbandry Resources, Food Science College, TAAHC-SWU Medicinal Plant Joint R&D Center, Tibet Agriculture & Animal Husbandry University, Nyingchi, Tibet, China
| | - Xiaozhong Lan
- Tibetan Collaborative Innovation Center of Agricultural and Animal Husbandry Resources, Food Science College, TAAHC-SWU Medicinal Plant Joint R&D Center, Tibet Agriculture & Animal Husbandry University, Nyingchi, Tibet, China.
| |
Collapse
|
16
|
Liu Y, Nazir MF, He S, Li H, Pan Z, Sun G, Dai P, Wang L, Du X. Deltapine 15 contributes to the genomic architecture of modern upland cotton cultivars. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1401-1411. [PMID: 35146550 DOI: 10.1007/s00122-022-04042-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
Foundation parents play a critical role in the genetic constituents of the derived genotypes. Deltapine-15 (DLP-15), introduced to China in 1950, is one of the most commonly used parents for early breeding programs in China. However, the formation and inheritance patterns of genomic constituents have not been studied. Therefore, this study aimed at understanding and exploring the genomic architecture of 146 DLP-15 derived cultivars with a common foundation parent DLP-15. Population structure based on sequencing data clustered genotypes into two groups (G1 and G2) supported by principal component analysis. Further exploration led to the identification of Chr-A08 with significantly differentiated regions between two groups. Moreover, we identified genome-wide identity by descent (IBD) segments (840 segments) to understand the genomic inheritance pattern in DLP-15 derived cultivars, spanning the 20-95 Mb region on Chr-A08. Interestingly, Chr-A08 depicted a unique inheritance pattern from DLP-15 to its derived cultivars. IBD-segment-based haplotype analysis suggested significant differences among the two groups. Phenotypic trait association with DLP-derived haplotypes concerning Chr-A08 suggested a significant increase in yield and fiber quality. Furthermore, distinguished IBD segments overlapped with previously reported QTLs concerning fiber yield and quality. Our results systematically identified genomic signatures transmitted from the foundation parent DLP-15 to its derived cultivars and provided a basis for further exploiting excellent haplotypes associated with DLP-15.
Collapse
Affiliation(s)
- Yingfei Liu
- Institute of Cotton Research, State Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Mian Faisal Nazir
- Institute of Cotton Research, State Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, Hainan, China
| | - Shoupu He
- Institute of Cotton Research, State Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, Hainan, China
| | - Hongge Li
- Institute of Cotton Research, State Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Zhaoe Pan
- Institute of Cotton Research, State Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Gaofei Sun
- Anyang Institute of Technology, Anyang, 455000, Henan, China
| | - Panhong Dai
- Institute of Cotton Research, State Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Liyuan Wang
- Institute of Cotton Research, State Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Xiongming Du
- Institute of Cotton Research, State Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, Hainan, China.
| |
Collapse
|