51
|
Hinge VR, Shaikh IM, Chavhan RL, Deshmukh AS, Shelake RM, Ghuge SA, Dethe AM, Suprasanna P, Kadam US. Assessment of genetic diversity and volatile content of commercially grown banana (Musa spp.) cultivars. Sci Rep 2022; 12:7979. [PMID: 35562398 PMCID: PMC9106755 DOI: 10.1038/s41598-022-11992-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/04/2022] [Indexed: 11/23/2022] Open
Abstract
Banana is an important fruit crop in the tropics and subtropics; however, limited information on biomarkers and signature volatiles is available for selecting commercial cultivars. Clonal fidelity is a major contributor to banana yield and aroma; however, there are no useful biomarkers available to validate clonal fidelity. In this study, we performed the molecular profiling of 20 banana cultivars consisting of diploid (AA or AB) and triploid (AAA or AAB or ABB) genomic groups. We screened 200 molecular markers, of which 34 markers (11 RAPD, 11 ISSR, and 12 SSR) yielded unequivocally scorable biomarker profiles. About 75, 69, and 24 allelic loci per marker were detected for RAPD, ISSR, and SSR markers, respectively. The statistical analysis of molecular variance (AMOVA) exhibited a high genetic difference of 77% with a significant FST value of 0.23 (p < 0.001). Interestingly, the UBC-858 and SSR CNMPF-13 markers were unique to Grand Nain and Ardhapuri cultivars, respectively, which could be used for clonal fidelity analysis. Furthermore, the analysis of banana fruit volatilome using headspace solid-phase microextraction-gas chromatography-tandem mass spectrometry (HS-SPME-GCMS) revealed a total of fifty-four volatile compounds in nine banana cultivars with 56% of the total volatile compounds belonging to the ester group as the significant contributor of aroma. The study assumes significance with informative biomarkers and signature volatiles which could be helpful in breeding and for the authentic identification of commercial banana cultivars.
Collapse
Affiliation(s)
- Vidya R Hinge
- Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology (Vasantrao Naik Marathwada Agricultural University, Parbhani), Latur, Maharashtra, India
| | - Irfan M Shaikh
- Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology (Vasantrao Naik Marathwada Agricultural University, Parbhani), Latur, Maharashtra, India
| | - Rahul L Chavhan
- Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology (Vasantrao Naik Marathwada Agricultural University, Parbhani), Latur, Maharashtra, India
| | - Abhijit S Deshmukh
- Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology (Vasantrao Naik Marathwada Agricultural University, Parbhani), Latur, Maharashtra, India
| | - Rahul Mahadev Shelake
- Division of Applied Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam, 52828, Republic of Korea
| | - Sandip A Ghuge
- Agricultural Research Organization (ARO), The Volcani Institute, P. O. Box 15159, 7505101, Rishon LeZion, Israel
| | - Amol M Dethe
- Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology (Vasantrao Naik Marathwada Agricultural University, Parbhani), Latur, Maharashtra, India
| | - Penna Suprasanna
- Homi Bhabha National Institute (HBNI) and Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Center, Mumbai, India
| | - Ulhas Sopanrao Kadam
- Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology (Vasantrao Naik Marathwada Agricultural University, Parbhani), Latur, Maharashtra, India. .,Division of Applied Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam, 52828, Republic of Korea.
| |
Collapse
|
52
|
Liu K, Kabir N, Wei Z, Sun Z, Wang J, Qi J, Liu M, Liu J, Zhou K. Genome-wide identification and expression profile of GhGRF gene family in Gossypium hirsutum L.. PeerJ 2022; 10:e13372. [PMID: 35586135 PMCID: PMC9109687 DOI: 10.7717/peerj.13372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/12/2022] [Indexed: 01/13/2023] Open
Abstract
Background Cotton is the primary source of renewable natural fiber in the textile industry and an important biodiesel crop. Growth regulating factors (GRFs) are involved in regulating plant growth and development. Methods Using genome-wide analysis, we identified 35 GRF genes in Gossypium hirsutum. Results Chromosomal location information revealed an uneven distribution of GhGRF genes, with maximum genes on chromosomes A02, A05, and A12 from the At sub-genome and their corresponding D05 and D12 from the Dt sub-genome. In the phylogenetic tree, 35 GRF genes were divided into five groups, including G1, G2, G3, G4, and G5. The majority of GhGRF genes have two to three introns and three to four exons, and their deduced proteins contained conserved QLQ and WRC domains in the N-terminal end of GRFs in Arabidopsis and rice. Sequence logos revealed that GRF genes were highly conserved during the long-term evolutionary process. The CDS of the GhGRF gene can complement MiRNA396a. Moreover, most GhGRF genes transcripts developed high levels of ovules and fibers. Analyses of promoter cis-elements and expression patterns indicated that GhGRF genes play an essential role in regulating plant growth and development by coordinating the internal and external environment and multiple hormone signaling pathways. Our analysis indicated that GhGRFs are ideal target genes with significant potential for improving the molecular structure of cotton.
Collapse
Affiliation(s)
- Kun Liu
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, Henan, China
| | - Nosheen Kabir
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Zhenzhen Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Zhuojing Sun
- Development Center for Science and Technology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Jian Wang
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, Henan, China
| | - Jing Qi
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, Henan, China
| | - Miaoyang Liu
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, Henan, China
| | - Ji Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Kehai Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| |
Collapse
|
53
|
Ma J, Qi S, Yuan M, Zhao D, Zhang D, Feng J, Wang J, Li W, Song C, Wang T, Zeng Q, Wu J, Han D, Jiang L. A genome-wide association study revealed the genetic variation and candidate genes for grain copper content in bread wheat ( Triticum aestivum L.). Food Funct 2022; 13:5177-5188. [PMID: 35437565 DOI: 10.1039/d1fo04173h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
As an essential microelement, copper plays a crucial role in the human body. However, the grains of bread wheat, a major crop food, contain a low copper content. Here, a diversity panel of 443 wheat accessions cultivated in four environments was used to analyse grain copper content by ICAP-7000, and the genetic variation in grain copper content was examined using a 660 K single nucleotide polymorphism chip. Phenotypic analysis indicated that the grain copper content varied between 2.58 mg kg-1 and 13.65 mg kg-1. A genome-wide association study identified 12 QTLs associated with grain copper content that showed significance in at least two environments on chromosomes 1A, 1D, 3D, 4A, 5A, 5D, 6B, 6D, 7A and 7D. Through haplotype analysis, the phenotypic difference between the haplotypes of three genes, TraesCS5D01G282300, TraesCS6B01G052900 and TraesCS7D01G146600, showed significance (P ⩽ 0.05) in four environments. They were considered to be important candidate genes for grain copper content in wheat. In addition, we detected that the grain copper content gradually decreased with release years among wheat accessions in China, and the percentage of favourable alleles showed a similar trend. Analysing the changes in grain copper content with yield factors, we found that the dilute effect was mainly caused by thousand kernel weight. This study provides useful information on the genetic basis for grain copper content, and thus helps in improving the wheat grain quality.
Collapse
Affiliation(s)
- Jianhui Ma
- College of Life Science, Henan Normal University, Xinxiang 453007, Henan, People's Republic of China.
| | - Siyuan Qi
- College of Life Science, Henan Normal University, Xinxiang 453007, Henan, People's Republic of China.
| | - Meng Yuan
- College of Life Science, Henan Normal University, Xinxiang 453007, Henan, People's Republic of China. .,State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China.
| | - Dongyang Zhao
- College of Life Science, Henan Normal University, Xinxiang 453007, Henan, People's Republic of China.
| | - Daijing Zhang
- College of Life Science, Henan Normal University, Xinxiang 453007, Henan, People's Republic of China.
| | - Jinyuan Feng
- College of Life Science, Henan Normal University, Xinxiang 453007, Henan, People's Republic of China.
| | - Jianing Wang
- College of Life Science, Henan Normal University, Xinxiang 453007, Henan, People's Republic of China.
| | - Wei Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, People's Republic of China
| | - Chengxiang Song
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, People's Republic of China
| | - Tianlin Wang
- Henan Engineering Technology Research Center of Food Processing and Circulation Safety Control, College of Food Science and Technology, Henan Agricultural University, Zhengzhou 450002, Henan, People's Republic of China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China.
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China.
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China.
| | - Lina Jiang
- College of Life Science, Henan Normal University, Xinxiang 453007, Henan, People's Republic of China.
| |
Collapse
|
54
|
Zhang W, Yuan Q, Wu Y, Zhang J, Nie J. Genome-Wide Identification and Characterization of the CC-NBS-LRR Gene Family in Cucumber ( Cucumis sativus L.). Int J Mol Sci 2022; 23:ijms23095048. [PMID: 35563438 PMCID: PMC9099878 DOI: 10.3390/ijms23095048] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 04/26/2022] [Accepted: 04/29/2022] [Indexed: 12/10/2022] Open
Abstract
The NBS-LRR (NLR) gene family plays a pivotal role in regulating disease defense response in plants. Cucumber is one of the most important vegetable crops in the world, and various plant diseases, including powdery mildew (PM), cause severe losses in both cucumber productivity and quality annually. To characterize and understand the role of the CC-NBS-LRR(CNL) family of genes in disease defense response in cucumber plants, we performed bioinformatical analysis to characterize these genes systematically. We identified 33 members of the CNL gene family in cucumber plants, and they are distributed on each chromosome with chromosome 4 harboring the largest cluster of five different genes. The corresponding CNL family member varies in the number of amino acids and exons, molecular weight, theoretical isoelectric point (pI) and subcellular localization. Cis-acting element analysis of the CNL genes reveals the presence of multiple phytohormone, abiotic and biotic responsive elements in their promoters, suggesting that these genes might be responsive to plant hormones and stress. Phylogenetic and synteny analysis indicated that the CNL proteins are conserved evolutionarily in different plant species, and they can be divided into four subfamilies based on their conserved domains. MEME analysis and multiple sequence alignment showed that conserved motifs exist in the sequence of CNLs. Further DNA sequence analysis suggests that CsCNL genes might be subject to the regulation of different miRNAs upon PM infection. By mining available RNA-seq data followed by real-time quantitative PCR (qRT-PCR) analysis, we characterized expression patterns of the CNL genes, and found that those genes exhibit a temporospatial expression pattern, and their expression is also responsive to PM infection, ethylene, salicylic acid, and methyl jasmonate treatment in cucumber plants. Finally, the CNL genes targeted by miRNAs were predicted in cucumber plants. Our results in this study provided some basic information for further study of the functions of the CNL gene family in cucumber plants.
Collapse
Affiliation(s)
- Wanlu Zhang
- College of Horticulture Science, Zhejiang AF University, Hangzhou 311300, China; (W.Z.); (Q.Y.); (Y.W.); (J.Z.)
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Hangzhou 311300, China
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang AF University, Hangzhou 311300, China
| | - Qi Yuan
- College of Horticulture Science, Zhejiang AF University, Hangzhou 311300, China; (W.Z.); (Q.Y.); (Y.W.); (J.Z.)
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Hangzhou 311300, China
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang AF University, Hangzhou 311300, China
| | - Yiduo Wu
- College of Horticulture Science, Zhejiang AF University, Hangzhou 311300, China; (W.Z.); (Q.Y.); (Y.W.); (J.Z.)
| | - Jing Zhang
- College of Horticulture Science, Zhejiang AF University, Hangzhou 311300, China; (W.Z.); (Q.Y.); (Y.W.); (J.Z.)
| | - Jingtao Nie
- College of Horticulture Science, Zhejiang AF University, Hangzhou 311300, China; (W.Z.); (Q.Y.); (Y.W.); (J.Z.)
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Hangzhou 311300, China
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang AF University, Hangzhou 311300, China
- Correspondence:
| |
Collapse
|
55
|
Ren T, Xie D, Peng C, Gui L, Price M, Zhou S, He X. Molecular evolution and phylogenetic relationships of Ligusticum (Apiaceae) inferred from the whole plastome sequences. BMC Ecol Evol 2022; 22:55. [PMID: 35501703 PMCID: PMC9063207 DOI: 10.1186/s12862-022-02010-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 04/21/2022] [Indexed: 12/04/2022] Open
Abstract
Background The genus Ligusticum belongs to Apiaceae, and its taxonomy has long been a major difficulty. A robust phylogenetic tree is the basis of accurate taxonomic classification of Ligusticum. We herein used 26 (including 14 newly sequenced) plastome-scale data to generate reliable phylogenetic trees to explore the phylogenetic relationships of Chinese Ligusticum. Results We found that these plastid genomes exhibited diverse plastome characteristics across all four currently identified clades in China, while the plastid protein-coding genes were conserved. The phylogenetic analyses by the concatenation and coalescent methods obtained a more robust molecular phylogeny than prior studies and showed the non-monophyly of Chinese Ligusticum. In the concatenation-based phylogeny analyses, the two datasets yielded slightly different topologies that may be primarily due to the discrepancy in the number of variable sites. Conclusions Our plastid phylogenomics analyses emphasized that the current circumscription of the Chinese Ligusticum should be reduced, and the taxonomy of Ligusticum urgently needs revision. Wider taxon sampling including the related species of Ligusticum will be necessary to explore the phylogenetic relationships of this genus. Overall, our study provided new insights into the taxonomic classification of Ligusticum and would serve as a framework for future studies on taxonomy and delimitation of Ligusticum from the perspective of the plastid genome. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02010-z.
Collapse
|
56
|
Jha UC, Nayyar H, Parida SK, Bakır M, von Wettberg EJB, Siddique KHM. Progress of Genomics-Driven Approaches for Sustaining Underutilized Legume Crops in the Post-Genomic Era. Front Genet 2022; 13:831656. [PMID: 35464848 PMCID: PMC9021634 DOI: 10.3389/fgene.2022.831656] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/24/2022] [Indexed: 12/22/2022] Open
Abstract
Legume crops, belonging to the Fabaceae family, are of immense importance for sustaining global food security. Many legumes are profitable crops for smallholder farmers due to their unique ability to fix atmospheric nitrogen and their intrinsic ability to thrive on marginal land with minimum inputs and low cultivation costs. Recent progress in genomics shows promise for future genetic gains in major grain legumes. Still it remains limited in minor legumes/underutilized legumes, including adzuki bean, cluster bean, horse gram, lathyrus, red clover, urd bean, and winged bean. In the last decade, unprecedented progress in completing genome assemblies of various legume crops and resequencing efforts of large germplasm collections has helped to identify the underlying gene(s) for various traits of breeding importance for enhancing genetic gain and contributing to developing climate-resilient cultivars. This review discusses the progress of genomic resource development, including genome-wide molecular markers, key breakthroughs in genome sequencing, genetic linkage maps, and trait mapping for facilitating yield improvement in underutilized legumes. We focus on 1) the progress in genomic-assisted breeding, 2) the role of whole-genome resequencing, pangenomes for underpinning the novel genomic variants underlying trait gene(s), 3) how adaptive traits of wild underutilized legumes could be harnessed to develop climate-resilient cultivars, 4) the progress and status of functional genomics resources, deciphering the underlying trait candidate genes with putative function in underutilized legumes 5) and prospects of novel breeding technologies, such as speed breeding, genomic selection, and genome editing. We conclude the review by discussing the scope for genomic resources developed in underutilized legumes to enhance their production and play a critical role in achieving the "zero hunger" sustainable development goal by 2030 set by the United Nations.
Collapse
Affiliation(s)
- Uday Chand Jha
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, India
| | | | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Melike Bakır
- Department of Agricultural Biotechnology, Faculty of Agriculture, Erciyes University, Kayseri, Turkey
| | - Eric J. B. von Wettberg
- Plant and Soil Science and Gund Institute for the Environment, The University of Vermont, Burlington, VT, United States
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | | |
Collapse
|
57
|
Ali M, Ahmad H, Amin B, Atif MJ, Cheng Z. Induce defense response of DADS in eggplants during the biotrophic phase of Verticillium dahliae. BMC PLANT BIOLOGY 2022; 22:172. [PMID: 35379184 PMCID: PMC8981950 DOI: 10.1186/s12870-022-03527-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
PURPOSE Verticillium wilt is a destructive vascular disease in eggplants. The complex defensive mechanisms of eggplant against this disease are very limited. METHODS Our work examined the bioactive properties of garlic allelochemical diallyl disulfide (DADS) as potential biostimulants for defense against V. dahliae in eggplant seedlings. We, therefore, foliar sprayed DADS on eggplants to study the defense response during the early biotrophic phase of V. dahliae (a hemibiotroph). RESULTS DADS application significantly increased root peroxidase (POD), phenylalanine-ammonia lyase (PAL) enzyme activity, and reduced H2O2 levels after 24 h of fungal inoculation. Salicylic acid (SA) in leaves and roots was significantly increased while, the jasmonic acid (JA), indole acetic acid (IAA), and abscisic acid (ABA) levels were decreased. The microscopic examinations of V. dahliae infection in roots displayed that the progression of infection was restricted in DADS-treated plants. Depositions of lignin and phenolic compounds such as ferulic acid, p-coumaric acid, and caffeic acid content were significantly higher in DADS-treated plants at 48 h post-inoculation. Similarly, the DADS application up-regulated pathogenesis-related (PR1, PR2, and PR5), mitogen-activated protein kinase (MPK1), and lipoxygenase (LOX) genes. Furthermore, DADS-treated plants exhibited a lower disease severity index (23.3% vs. 57.0% in controls), indicating successful defense against V. dahliae. CONCLUSIONS Our findings concluded that the biological function of garlic allelochemical DADS has a prominent role in the higher defense resistance of eggplants during the early infection of V. dahliae.
Collapse
Affiliation(s)
- Muhammad Ali
- Department of Vegetable Science, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Husain Ahmad
- Department of Vegetable Science, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Bakht Amin
- Department of Vegetable Science, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Muhammad Jawaad Atif
- Department of Vegetable Science, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhihui Cheng
- Department of Vegetable Science, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| |
Collapse
|
58
|
Bo K, Duan Y, Qiu X, Zhang M, Shu Q, Sun Y, He Y, Shi Y, Weng Y, Wang C. Promoter variation in a homeobox gene, CpDll, is associated with deeply lobed leaf in Cucurbita pepo L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1223-1234. [PMID: 34985539 DOI: 10.1007/s00122-021-04026-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
CpDll, encoding an HD-Zip I transcription factor, positively regulates formation of deeply lobed leaf shape in zucchini, Cucurbita pepo, which is associated with sequence variation in its promoter region. Leaf shape is an important horticultural trait in zucchini (Cucurbita pepo L.). Deeply lobed leaves have potential advantages for high-density planting and hybrid production. However, little is known about the molecular basis of deeply lobed leaf formation in this important vegetable crop. Here, we conducted QTL analysis and fine mapping of the deeply lobed leaf (CpDll) locus using recombinant inbred lines and large F2 populations developed from crosses between the deeply lobed leaf HM-S2, and entire leaf Jin-GL parental lines. We show that CpDll exhibited incomplete dominance for the deeply lobed leaf shape in HM-S2. Map-based cloning provided evidence that CpCll encodes a type I homeodomain (HD)- and Leu zipper (Zip) element-containing transcription factor. Sequence analysis between HM-S2 and Jin-GL revealed no sequence variations in the coding sequences, whereas a number of variations were identified in the promoter region between them. DUAL-LUC assays revealed significantly stronger promoter activity in HM-S2 than that in Jin-GL. There was also significantly higher expression of CpDll in the leaf base of deeply lobed leaves of HM-S2 compared with entire leaf Jin-GL. Comparative analysis of CpDll gene homologs in nine cucurbit crop species (family Cucurbitaceae) revealed conservation in both structure and function of this gene in regulation of deeply lobed leaf formation. Our work provides new insights into the molecular basis of leaf lobe formation in pumpkin/squash and other cucurbit crops. This work also facilitates marker-assisted selection for leaf shape in zucchini breeding.
Collapse
Affiliation(s)
- Kailiang Bo
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Ying Duan
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Xiyan Qiu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Meng Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Qin Shu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Yapei Sun
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Yadi He
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Yuzi Shi
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Yiqun Weng
- USDA-ARS Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA.
| | - Changlin Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China.
- China Vegetable Biotechnology (Shouguang) Co., Ltd, Shouguang, Shandong, People's Republic of China.
| |
Collapse
|
59
|
Harrison K, Levy JG, Tamborindeguy C. Effects of 'Candidatus Liberibacter solanacearum' haplotypes A and B on tomato gene expression and geotropism. BMC PLANT BIOLOGY 2022; 22:156. [PMID: 35354405 PMCID: PMC8966271 DOI: 10.1186/s12870-022-03505-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND The tomato psyllid, Bactericera cockerelli Šulc (Hemiptera: Triozidae), is a pest of solanaceous crops such as tomato (Solanum lycopersicum L.) in the U.S. and vectors the disease-causing pathogen 'Candidatus Liberibacter solanacearum' (or Lso). Disease symptom severity is dependent on Lso haplotype: tomato plants infected with Lso haplotype B experience more severe symptoms and higher mortality compared to plants infected with Lso haplotype A. By characterizing the molecular differences in the tomato plant's responses to Lso haplotypes, the key components of LsoB virulence can be identified and, thus, targeted for disease mitigation strategies. RESULTS To characterize the tomato plant genes putatively involved in the differential immune responses to Lso haplotypes A and B, RNA was extracted from tomato 'Moneymaker' leaves 3 weeks after psyllid infestation. Gene expression levels were compared between uninfected tomato plants (i.e., controls and plants infested with Lso-free psyllids) and infected plants (i.e., plants infested with psyllids infected with either Lso haplotype A or Lso haplotype B). Furthermore, expression levels were compared between plants infected with Lso haplotype A and plants infected with Lso haplotype B. A whole transcriptome analysis identified 578 differentially expressed genes (DEGs) between uninfected and infected plants as well as 451 DEGs between LsoA- and LsoB-infected plants. These DEGs were primarily associated with plant defense against abiotic and biotic stressors, growth/development, plant primary metabolism, transport and signaling, and transcription/translation. These gene expression changes suggested that tomato plants traded off plant growth and homeostasis for improved defense against pathogens, especially when infected with LsoB. Consistent with these results, tomato plant growth experiments determined that LsoB-infected plants were significantly stunted and had impaired negative geotropism. However, it appeared that the defense responses mounted by tomatoes were insufficient for overcoming the disease symptoms and mortality caused by LsoB infection, while these defenses could compensate for LsoA infection. CONCLUSION The transcriptomic analysis and growth experiments demonstrated that Lso-infected tomato plants underwent gene expression changes related to abiotic and biotic stressors, impaired growth/development, impaired plant primary metabolism, impaired transport and signaling transduction, and impaired transcription/translation. Furthermore, the transcriptomic analysis also showed that LsoB-infected plants, relative to LsoA-infected, experienced more severe stunting, had improved responses to some stressors and impaired responses to others, had poorer transport and signaling transduction, and had impaired carbohydrate synthesis and photosynthesis.
Collapse
Affiliation(s)
- Kyle Harrison
- Department of Horticultural Sciences, Texas A&M University, College station, TX 77843, USA
- Present address: USDA-ARS, Agroecosystem Management Research, Lincoln, NE, 68503, USA
| | - Julien G Levy
- Department of Horticultural Sciences, Texas A&M University, College station, TX 77843, USA.
| | | |
Collapse
|
60
|
Bassetti N, Caarls L, Bukovinszkine'Kiss G, El-Soda M, van Veen J, Bouwmeester K, Zwaan BJ, Schranz ME, Bonnema G, Fatouros NE. Genetic analysis reveals three novel QTLs underpinning a butterfly egg-induced hypersensitive response-like cell death in Brassica rapa. BMC PLANT BIOLOGY 2022; 22:140. [PMID: 35331150 PMCID: PMC8944062 DOI: 10.1186/s12870-022-03522-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Cabbage white butterflies (Pieris spp.) can be severe pests of Brassica crops such as Chinese cabbage, Pak choi (Brassica rapa) or cabbages (B. oleracea). Eggs of Pieris spp. can induce a hypersensitive response-like (HR-like) cell death which reduces egg survival in the wild black mustard (B. nigra). Unravelling the genetic basis of this egg-killing trait in Brassica crops could improve crop resistance to herbivory, reducing major crop losses and pesticides use. Here we investigated the genetic architecture of a HR-like cell death induced by P. brassicae eggs in B. rapa. RESULTS A germplasm screening of 56 B. rapa accessions, representing the genetic and geographical diversity of a B. rapa core collection, showed phenotypic variation for cell death. An image-based phenotyping protocol was developed to accurately measure size of HR-like cell death and was then used to identify two accessions that consistently showed weak (R-o-18) or strong cell death response (L58). Screening of 160 RILs derived from these two accessions resulted in three novel QTLs for Pieris brassicae-induced cell death on chromosomes A02 (Pbc1), A03 (Pbc2), and A06 (Pbc3). The three QTLs Pbc1-3 contain cell surface receptors, intracellular receptors and other genes involved in plant immunity processes, such as ROS accumulation and cell death formation. Synteny analysis with A. thaliana suggested that Pbc1 and Pbc2 are novel QTLs associated with this trait, while Pbc3 also contains an ortholog of LecRK-I.1, a gene of A. thaliana previously associated with cell death induced by a P. brassicae egg extract. CONCLUSIONS This study provides the first genomic regions associated with the Pieris egg-induced HR-like cell death in a Brassica crop species. It is a step closer towards unravelling the genetic basis of an egg-killing crop resistance trait, paving the way for breeders to further fine-map and validate candidate genes.
Collapse
Affiliation(s)
- Niccolò Bassetti
- Biosystematics Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Lotte Caarls
- Biosystematics Group, Wageningen University & Research, Wageningen, The Netherlands
- Laboratory of Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - Gabriella Bukovinszkine'Kiss
- Biosystematics Group, Wageningen University & Research, Wageningen, The Netherlands
- Laboratory of Genetics, Wageningen University & Research, Wageningen, The Netherlands
| | - Mohamed El-Soda
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Jeroen van Veen
- Biosystematics Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Klaas Bouwmeester
- Biosystematics Group, Wageningen University & Research, Wageningen, The Netherlands
- Laboratory of Entomology, Wageningen University & Research, Wageningen, The Netherlands
| | - Bas J Zwaan
- Laboratory of Genetics, Wageningen University & Research, Wageningen, The Netherlands
| | - M Eric Schranz
- Biosystematics Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Guusje Bonnema
- Laboratory of Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - Nina E Fatouros
- Biosystematics Group, Wageningen University & Research, Wageningen, The Netherlands.
| |
Collapse
|
61
|
Huang S, Liu M, Chen G, Si F, Fan F, Guo Y, Yuan L, Yang F, Li S. Favorable QTLs from Oryza longistaminata improve rice drought resistance. BMC PLANT BIOLOGY 2022; 22:136. [PMID: 35321642 PMCID: PMC8941802 DOI: 10.1186/s12870-022-03516-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/07/2022] [Indexed: 05/14/2023]
Abstract
BACKGROUND Drought is the major abiotic stress to rice grain production under unpredictable changing climatic environments. Wild rice of O. longistaminata show diverse responses and strong tolerance to stress environments. In order to identify whether the O. longistaminata can improve the rice drought resistance or not, a BIL population of 143 BC2F20 lines derived from the cross between the cultivar rice 9311 and O. longistaminata were assessed under stress of 20% PEG6000. RESULTS In total, 28 QTLs related to drought resistance based on eight agronomic traits of seedlings were identified. Of which, thirteen QTLs including two QTLs for leaf drying, one QTL for leaf rolling, one QTL for leaf number, five QTLs for dry weight of root, two QTLs for dry weight of shoot, one QTL for maximum root length and two QTLs for maximum shoot length were derived from O. longistaminata. What's more, qDWR8.1 for dry weight of root was repeatedly detected and fine-mapped to an interval about 36.2 Kb. The unique allele of MH08g0242800 annotated as ATP-dependent Clp protease proteolytic subunit from O. longistaminata was suggested as the candidate gene for drought resistance. Further, six representative BIL lines were stably characterized showing significantly stronger drought resistance than 9311 based on principle component analysis, they each contained 2 ~ 5 QTLs including qDWR8.1 from O. longistaminata. CONCLUSIONS Together, our results indicate that the QTLs from O. longistaminata can effectively enhance the drought tolerance of rice, showing great potential value in breeding of elite rice varieties, which will lay a novel insight into the genetic network for drought tolerance of rice.
Collapse
Affiliation(s)
- Shaoying Huang
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, China
| | - Manman Liu
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, China
| | - Gaili Chen
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, China
| | - Fengfeng Si
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, China
| | - Fengfeng Fan
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, China
| | - Yu Guo
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, China
| | - Lei Yuan
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, China
| | - Fang Yang
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, China.
| | - Shaoqing Li
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, China.
| |
Collapse
|
62
|
Mancinotti D, Frick KM, Geu-Flores F. Biosynthesis of quinolizidine alkaloids in lupins: mechanistic considerations and prospects for pathway elucidation. Nat Prod Rep 2022; 39:1423-1437. [PMID: 35302146 DOI: 10.1039/d1np00069a] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: up to 2022Quinolizidine alkaloids (QAs) are a class of alkaloids that accumulate in a variety of leguminous plants and have applications in the agricultural, pharmaceutical and chemical industries. QAs are notoriously present in cultivated lupins (Lupinus spp.) where they complicate the use of the valuable, high-protein beans due to their toxic properties and bitter taste. Compared to many other alkaloid classes, the biosynthesis of QAs is poorly understood, with only the two first pathway enzymes having been discovered so far. In this article, we review the different biosynthetic hypotheses that have been put forth in the literature (1988-2009) and highlight one particular hypothesis (1988) that agrees with the often ignored precursor feeding studies (1964-1994). Our focus is on the biosynthesis of the simple tetracyclic QA (-)-sparteine, from which many of the QAs found in lupins derive. We examine every pathway step on the way to (-)-sparteine and discuss plausible mechanisms, altogether proposing the involvement of 6-9 enzymes. Together with the new resources for gene discovery developed for lupins in the past few years, this review will contribute to the full elucidation of the QA pathway, including the identification and characterization of the missing pathway enzymes.
Collapse
Affiliation(s)
- Davide Mancinotti
- Section for Plant Biochemistry and Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Denmark.
| | - Karen Michiko Frick
- Section for Plant Biochemistry and Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Denmark.
| | - Fernando Geu-Flores
- Section for Plant Biochemistry and Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Denmark.
| |
Collapse
|
63
|
Malik P, Kumar J, Sharma S, Meher PK, Balyan HS, Gupta PK, Sharma S. GWAS for main effects and epistatic interactions for grain morphology traits in wheat. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:651-668. [PMID: 35465203 PMCID: PMC8986918 DOI: 10.1007/s12298-022-01164-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 03/05/2022] [Accepted: 03/07/2022] [Indexed: 06/05/2023]
Abstract
In the present study in wheat, GWAS was conducted for identification of marker trait associations (MTAs) for the following six grain morphology traits: (1) grain cross-sectional area (GCSA), (2) grain perimeter (GP), (3) grain length (GL), (4) grain width (GWid), (5) grain length-width ratio (GLWR) and (6) grain form-density (GFD). The data were recorded on a subset of spring wheat reference set (SWRS) comprising 225 diverse genotypes, which were genotyped using 10,904 SNPs and phenotyped for two consecutive years (2017-2018, 2018-2019). GWAS was conducted using five different models including two single-locus models (CMLM, SUPER), one multi-locus model (FarmCPU), one multi-trait model (mvLMM) and a model for Q x Q epistatic interactions. False discovery rate (FDR) [P value -log10(p) ≥ 5] and Bonferroni correction [P value -log10(p) ≥ 6] (corrected p value < 0.05) were applied to eliminate false positives due to multiple testing. This exercise gave 88 main effect and 29 epistatic MTAs after FDR and 13 main effect and 6 epistatic MTAs after Bonferroni corrections. MTAs obtained after Bonferroni corrections were further utilized for identification of 55 candidate genes (CGs). In silico expression analysis of CGs in different tissues at different parts of the seed at different developmental stages was also carried out. MTAs and CGs identified during the present study are useful addition to available resources for MAS to supplement wheat breeding programmes after due validation and also for future strategic basic research. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-022-01164-w.
Collapse
Affiliation(s)
- Parveen Malik
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, U.P 250 004 India
| | - Jitendra Kumar
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, U.P 250 004 India
- Department of Biotechnology, National Agri-Food Biotechnology Institute (NABI), Govt. of India, Sector 81 (Knowledge City), S.A.S. Nagar, Mohali, Punjab 140306 India
| | - Shiveta Sharma
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, U.P 250 004 India
| | - Prabina Kumar Meher
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012 India
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, U.P 250 004 India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, U.P 250 004 India
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, U.P 250 004 India
| |
Collapse
|
64
|
Unravelling the treasure trove of drought-responsive genes in wild-type peanut through transcriptomics and physiological analyses of root. Funct Integr Genomics 2022; 22:215-233. [PMID: 35195841 DOI: 10.1007/s10142-022-00833-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 11/04/2022]
Abstract
Peanut is one of the most valuable legumes, grown mainly in arid and semi-arid regions, where its production may be hindered by the lack of water. Therefore, breeding drought tolerant varieties is of great importance for peanut breeding programs around the world. Unlike cultivated peanuts, wild peanuts have greater genetic diversity and are an important source of alleles conferring tolerance/resistance to abiotic and biotic stresses. To decipher the transcriptome changes under drought stress, transcriptomics of roots of highly tolerant Arachis duranensis (ADU) and moderately susceptible A. stenosperma (AST) genotypes were performed. Transcriptome analysis revealed an aggregate of 1465 differentially expressed genes (DEGs), and among the identified DEGs, there were 366 single nucleotide polymorphisms (SNPs). Gene ontology and Mapman analyses revealed that the ADU genotype had a higher number of transcripts related to DNA methylation or demethylation, phytohormone signal transduction and flavonoid production, transcription factors, and responses to ethylene. The transcriptome analysis was endorsed by qRT-PCR, which showed a strong correlation value (R2 = 0.96). Physio-biochemical analysis showed that the drought-tolerant plants produced more osmolytes, ROS phagocytes, and sugars, but less MDA, thus attenuating the effects of drought stress. In addition, three SNPs of the gene encoding transcription factor NFAY (Aradu.YE2F8), expansin alpha (Aradu.78HGD), and cytokinin dehydrogenase 1-like (Aradu.U999X) exhibited polymorphism in selected different genotypes. Such SNPs could be useful for the selection of drought-tolerant genotypes.
Collapse
|
65
|
Kaur S, Samota MK, Choudhary M, Choudhary M, Pandey AK, Sharma A, Thakur J. How do plants defend themselves against pathogens-Biochemical mechanisms and genetic interventions. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:485-504. [PMID: 35400890 PMCID: PMC8943088 DOI: 10.1007/s12298-022-01146-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 02/04/2022] [Accepted: 02/06/2022] [Indexed: 05/15/2023]
Abstract
In agro-ecosystem, plant pathogens hamper food quality, crop yield, and global food security. Manipulation of naturally occurring defense mechanisms in host plants is an effective and sustainable approach for plant disease management. Various natural compounds, ranging from cell wall components to metabolic enzymes have been reported to protect plants from infection by pathogens and hence provide specific resistance to hosts against pathogens, termed as induced resistance. It involves various biochemical components, that play an important role in molecular and cellular signaling events occurring either before (elicitation) or after pathogen infection. The induction of reactive oxygen species, activation of defensive machinery of plants comprising of enzymatic and non-enzymatic antioxidative components, secondary metabolites, pathogenesis-related protein expression (e.g. chitinases and glucanases), phytoalexin production, modification in cell wall composition, melatonin production, carotenoids accumulation, and altered activity of polyamines are major induced changes in host plants during pathogen infection. Hence, the altered concentration of biochemical components in host plants restricts disease development. Such biochemical or metabolic markers can be harnessed for the development of "pathogen-proof" plants. Effective utilization of the key metabolites-based metabolic markers can pave the path for candidate gene identification. This present review discusses the valuable information for understanding the biochemical response mechanism of plants to cope with pathogens and genomics-metabolomics-based sustainable development of pathogen proof cultivars along with knowledge gaps and future perspectives to enhance sustainable agricultural production.
Collapse
Affiliation(s)
- Simardeep Kaur
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Manoj Choudhary
- ICAR-National Research Center for Integrated Pest Management, New Delhi, India
- Department of Plant Pathology, University of Florida, Gainesville, United States
| | - Mukesh Choudhary
- School of Agriculture and Environment, The University of Western Australia, Perth, Australia
- ICAR-Indian Institute of Maize Research, PAU Campus, Ludhiana, India
| | - Abhay K. Pandey
- Department of Mycology and Microbiology, Tea Research Association-North Bengal Regional R & D Center, Nagrakata, West Bengal 735225 India
| | - Anshu Sharma
- Department of FST, Dr. YS Parmar UHF Nauni, Solan, India
| | - Julie Thakur
- Department of Botany, Bhaskaracharya College of Applied Sciences, University of Delhi, Delhi, India
| |
Collapse
|
66
|
Kabir N, Zhang X, Liu L, Qanmber G, Zhang L, Wang YX, Sun Z, Zhao N, Wang G. RAD gene family analysis in cotton provides some key genes for flowering and stress tolerance in upland cotton G. hirsutum. BMC Genomics 2022; 23:40. [PMID: 35012446 PMCID: PMC8744286 DOI: 10.1186/s12864-021-08248-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/09/2021] [Indexed: 12/25/2022] Open
Abstract
Background RADIALIS (RAD), belongs to the MYB gene family and regulates a variety of functions including floral dorsoventral asymmetry in Antirrhinum majus and development of fruit proteins in Solanum lycopersicum. RAD genes contain an SNF2_N superfamily domain. Here, we comprehensively identified 68 RAD genes from six different species including Arabidopsis and five species of cotton. Results Phylogenetic analysis classified RAD genes into five groups. Gene structure, protein motifs and conserved amino acid residues indicated that GhRAD genes were highly conserved during the evolutionary process. Chromosomal location information showed that GhRAD genes were distributed unevenly on different chromosomes. Collinearity and selection pressure analysis indicated RAD gene family expansion in G. hirsutum and G. barbadense with purifying selection pressure. Further, various growth and stress related promotor cis-acting elements were observed. Tissue specific expression level indicated that most GhRAD genes were highly expressed in roots and flowers (GhRAD2, GhRAD3, GhRAD4 and GhRAD11). Next, GhRAD genes were regulated by phytohormonal stresses (JA, BL and IAA). Moreover, Ghi-miRN1496, Ghi-miR1440, Ghi-miR2111b, Ghi-miR2950a, Ghi-miR390a, Ghi-miR390b and Ghi-miR7495 were the miRNAs targeting most of GhRAD genes. Conclusions Our study revealed that RAD genes are evolutionary conserved and might be involved in different developmental processes and hormonal stress response. Data presented in our study could be used as the basis for future studies of RAD genes in cotton. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08248-z.
Collapse
Affiliation(s)
- Nosheen Kabir
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Xin Zhang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Henan, 450001, Zhengzhou, China
| | - Le Liu
- Xinjiang Production & Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Biotechnology Research Institute of Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China
| | - Ghulam Qanmber
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Lian Zhang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Henan, 450001, Zhengzhou, China
| | - Yu Xuan Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Zhuojing Sun
- Development Center for Science and Technology, Ministry of Agriculture and Rural Affairs, Beijing, 100122, China
| | - Na Zhao
- Xinjiang Production & Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Biotechnology Research Institute of Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China.
| | - Gang Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Henan, 450001, Zhengzhou, China.
| |
Collapse
|
67
|
Han X, Wei X, Lu W, Wu Q, Mao L, Luo Z. Transcriptional regulation of KCS gene by bZIP29 and MYB70 transcription factors during ABA-stimulated wound suberization of kiwifruit (Actinidia deliciosa). BMC PLANT BIOLOGY 2022; 22:23. [PMID: 34998386 PMCID: PMC8742354 DOI: 10.1186/s12870-021-03407-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/09/2021] [Indexed: 05/05/2023]
Abstract
BACKGROUND Our previous study has demonstrated that the transcription of AchnKCS involved in suberin biosynthesis was up-regulated by exogenous abscisic acid (ABA) during the wound suberization of kiwifruit, but the regulatory mechanism has not been fully elucidated. RESULTS Through subcellular localization analysis in this work, AchnbZIP29 and AchnMYB70 transcription factors were observed to be localized in the nucleus. Yeast one-hybrid and dual-luciferase assay proved the transcriptional activation of AchnMYB70 and transcriptional suppression of AchnbZIP29 on AchnKCS promoter. Furthermore, the transcription level of AchnMYB70 was enhanced by ABA during wound suberization of kiwifruit, but AchnbZIP29 transcription was reduced by ABA. CONCLUSIONS Therefore, it was believed that ABA enhanced the transcriptional activation of AchnMYB70 on AchnKCS by increasing AchnMYB70 expression. On the contrary, ABA relieved the inhibitory effect of AchnbZIP29 on transcription of AchnKCS by inhibiting AchnbZIP29 expression. These results gave further insight into the molecular regulatory network of ABA in wound suberization of kiwifruit.
Collapse
Affiliation(s)
- Xueyuan Han
- School of Life Science, Shaoxing University, Shaoxing, 312000, Zhejiang Province, China
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory of Agro-Food Processing, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, 310058, China
| | - Xiaopeng Wei
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory of Agro-Food Processing, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, 310058, China
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, 450002, Henan, China
| | - Wenjing Lu
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory of Agro-Food Processing, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, 310058, China
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Qiong Wu
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou, 450001, China
| | - Linchun Mao
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory of Agro-Food Processing, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, 310058, China.
- Ningbo Research Institute, Zhejiang University, Ningbo, 315100, China.
| | - Zisheng Luo
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory of Agro-Food Processing, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, 310058, China
- Ningbo Research Institute, Zhejiang University, Ningbo, 315100, China
| |
Collapse
|
68
|
Sabir IA, Manzoor MA, Shah IH, Liu X, Zahid MS, Jiu S, Wang J, Abdullah M, Zhang C. MYB transcription factor family in sweet cherry (Prunus avium L.): genome-wide investigation, evolution, structure, characterization and expression patterns. BMC PLANT BIOLOGY 2022; 22:2. [PMID: 34979911 PMCID: PMC8722155 DOI: 10.1186/s12870-021-03374-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/01/2021] [Indexed: 05/10/2023]
Abstract
BACK GROUND MYB Transcription factors (TFs) are most imperative and largest gene family in plants, which participate in development, metabolism, defense, differentiation and stress response. The MYB TFs has been studied in various plant species. However, comprehensive studies of MYB gene family in the sweet cherry (Prunus avium L.) are still unknown. RESULTS In the current study, a total of 69 MYB genes were investigated from sweet cherry genome and classified into 28 subfamilies (C1-C28 based on phylogenetic and structural analysis). Microcollinearity analysis revealed that dispersed duplication (DSD) events might play an important role in the MYB genes family expansion. Chromosomal localization, the synonymous (Ks) and nonsynonymous (Ka) analysis, molecular characteristics (pI, weight and length of amino acids) and subcellular localization were accomplished using several bioinformatics tools. Furthermore, the members of distinct subfamilies have diverse cis-acting regions, conserved motifs, and intron-exon architectures, indicating functional heterogeneity in the MYB family. Moreover, the transcriptomic data exposed that MYB genes might play vital role in bud dormancy. The quantitative real-time qRT-PCR was carried out and the expression pattern indicated that MYB genes significantly expressed in floral bud as compared to flower and fruit. CONCLUSION Our comprehensive findings provide supportive insights into the evolutions, expansion complexity and functionality of PavMYB genes. These PavMYB genes should be further investigated as they seem to be brilliant candidates for dormancy manipulation in sweet cherry.
Collapse
Affiliation(s)
- Irfan Ali Sabir
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | | | - Iftikhar Hussain Shah
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xunju Liu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Muhmmad Salman Zahid
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Songtao Jiu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiyuan Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Muhammad Abdullah
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Caixi Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
| |
Collapse
|
69
|
Kabir N, Lin H, Kong X, Liu L, Qanmber G, Wang Y, Zhang L, Sun Z, Yang Z, Yu Y, Zhao N. Identification, evolutionary analysis and functional diversification of RAV gene family in cotton (G. hirsutum L.). PLANTA 2021; 255:14. [PMID: 34862931 DOI: 10.1007/s00425-021-03782-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
Genome wide analysis, expression pattern analysis, and functional characterization of RAV genes highlight their roles in roots, stem development and hormonal response. RAV (Related to ABI3 and VP1) gene family members have been involved in tissues/organs growth and hormone signaling in various plant species. Here, we identified 247 RAVs from 12 different species with 33 RAV genes from G. hirsutum. Phylogenetic analysis classified RAV genes into four distinct groups. Analysis of gene structure showed that most GhRAVs lack introns. Motif distribution pattern and protein sequence logos indicated that GhRAV genes were highly conserved during the process of evolution. Promotor cis-acting elements revealed that promotor regions of GhRAV genes encode numerous elements related to plant growth, abiotic stresses and phytohormones. Chromosomal location information showed uneven distribution of 33 GhRAV genes on different chromosomes. Collinearity analysis identified 628 and 52 orthologous/ paralogous gene pairs in G. hirsutum and G. barbadense, respectively. Ka/Ks values indicated that GhRAV and GbRAV genes underwent strong purifying selection pressure. Selecton model and codon model selection revealed that GhRAV amino acids were under purifying selection and adaptive evolution exists among GhRAV proteins. Three dimensional structure of GhRAVs indicated the presence of numerous alpha helix and beta-barrels. Expression level revealed that some GhRAV genes exhibited high expression in roots (GhRAV3, GhRAV4, GhRAV11, GhRAV18, GhRAV20 and GhRAV30) and stem (GhRAV3 and GhRAV18), indicating their potential role in roots and stem development. GhRAV genes can be regulated by phytohormonal stresses (BL, JA and IAA). Our study provides a reference for future studies related to the functional analysis of GhRAVs in cotton.
Collapse
Affiliation(s)
- Nosheen Kabir
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Hai Lin
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute of Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China
| | - Xianhui Kong
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute of Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China
| | - Le Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Ghulam Qanmber
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - YuXuan Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Lian Zhang
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute of Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China
| | - Zhuojing Sun
- Development Center for Science and Technology, Ministry of Agriculture and Rural Affairs, Beijing, 100122, China
| | - Zuoren Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute of Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China
| | - Yu Yu
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute of Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China.
| | - Na Zhao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| |
Collapse
|
70
|
Chattopadhyay K, Chakraborty K, Samal P, Sarkar RK. Identification of QTLs for stagnant flooding tolerance in rice employing genotyping by sequencing of a RIL population derived from Swarna × Rashpanjor. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2893-2909. [PMID: 35035143 PMCID: PMC8720131 DOI: 10.1007/s12298-021-01107-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 11/15/2021] [Accepted: 11/23/2021] [Indexed: 05/04/2023]
Abstract
UNLABELLED In lowland rice ecosystems stagnant flooding or partial submergence has a significant negative impact on important yield attributing traits resulting in substantial grain yield reduction. Genetics of this stress is not yet studied intensively. Rashpanjor (IC 575321), a landrace from India, was identified and used as the tolerant donor for stagnant flooding and was crossed with high yielding variety Swarna to develop the RIL population for the present investigation. Yield and yield attributing traits of 180 F2:8 lines in rainfed non-stressed and stressed (stagnant flooding with 45 ± 5 cm standing water) conditions were recorded in the wet season of 2018 and stress susceptibility and tolerance indices of yield component traits were deduced. Homo-polymorphic high-quality SNPs between two parents derived from genotyping by sequencing were employed and 17 putative QTLs for plant height, shoot elongation, panicle number, grain weight, panicle length in control and stagnant flooding conditions were identified. Tolerance and susceptibility indexes for these traits were detected in chromosomes 1, 3, 4, 5, 6, 10, 11, and 12 with PVE ranging from 6.53 to 57.89%. Two major QTLs clusters were found for stress susceptibility index of grain and panicle weight on chromosome 1 and plant height in non-stress condition and stress tolerance index of elongation ability on chromosome 3. Putative functional genes present either in associated non-synonymous SNPs or inside the QTL regions were also predicted. Some of them were directly associated with ethylene biosynthesis and encoding auxin responsive factors for better adaptation under stagnant flooding and also coded for different transcription factors viz. NAC domain-binding protein, WRKY gene family, and MYB class known for ROS scavenging and production of metabolites to enhance tolerance to stagnant flooding. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01107-x.
Collapse
Affiliation(s)
| | - Koushik Chakraborty
- Division of Crop Physiology and Biochemistry, ICAR-National Rice Research Institute, Cuttack, India
| | - Prabhudatta Samal
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, India
| | - Ramani Kumar Sarkar
- Division of Crop Physiology and Biochemistry, ICAR-National Rice Research Institute, Cuttack, India
| |
Collapse
|
71
|
Pal N, Saini DK, Kumar S. Meta-QTLs, ortho-MQTLs and candidate genes for the traits contributing to salinity stress tolerance in common wheat ( Triticum aestivum L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2767-2786. [PMID: 35035135 PMCID: PMC8720133 DOI: 10.1007/s12298-021-01112-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 12/04/2021] [Accepted: 12/07/2021] [Indexed: 05/20/2023]
Abstract
A meta-analysis of QTLs associated with the traits contributing to salinity tolerance was undertaken in wheat to detect consensus and robust meta-QTLs (MQTLs) using 844 known QTLs retrieved from 26 earlier studies. A consensus map with a total length of 4621.56 cM including 7710 markers was constructed using 21 individual linkage maps and three previously published integrated genetic maps. Out of 844 QTLs, 571 QTLs were projected on the consensus map which gave origin to 100 MQTLs. Interestingly, 49 MQTLs were co-located with marker-trait associations reported in wheat genome-wide association studies for the traits contributing to salinity stress tolerance. Five potential MQTLs associated with the major salinity-responsive traits were also identified to be utilized in the breeding programme. In the resulted MQTLs, the average confidence interval (CI, 3.58 cM) was reduced up to 4.16 folds compared to the mean CI of the initial QTLs. Furthermore, as many as 617 gene models including 81 most likely candidate genes (CGs) were identified in the high confidence MQTL regions. These most likely CGs encoded proteins mainly belonging to the following families: B-box-type zinc finger, cytochrome P450 protein, pentatricopeptide repeat, phospholipid/glycerol acyltransferase, F-box protein, small auxin-up RNA, UDP-glucosyltransferase, glutathione S-transferase protein, etc. In addition, ortho-MQTL analysis based on synteny among wheat, rice and barley was also performed which permitted the identification of six ortho-MQTLs among these three cereals. This meta-analysis defines a genome-wide landscape on the most stable and consistent loci associated with reliable molecular markers and candidate genes for salinity tolerance in wheat. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01112-0.
Collapse
Affiliation(s)
- Neeraj Pal
- Department of Molecular Biology and Genetic Engineering, G. B. Pant, University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab 141004 India
| | - Sundip Kumar
- Department of Molecular Biology and Genetic Engineering, G. B. Pant, University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| |
Collapse
|
72
|
Jan I, Saripalli G, Kumar K, Kumar A, Singh R, Batra R, Sharma PK, Balyan HS, Gupta PK. Meta-QTLs and candidate genes for stripe rust resistance in wheat. Sci Rep 2021; 11:22923. [PMID: 34824302 PMCID: PMC8617266 DOI: 10.1038/s41598-021-02049-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/02/2021] [Indexed: 11/15/2022] Open
Abstract
In bread wheat, meta-QTL analysis was conducted using 353 QTLs that were available from earlier studies. When projected onto a dense consensus map comprising 76,753 markers, only 184 QTLs with the required information, could be utilized leading to identification of 61 MQTLs spread over 18 of the 21 chromosomes (barring 5D, 6D and 7D). The range for mean R2 (PVE %) was 1.9% to 48.1%, and that of CI was 0.02 to 11.47 cM; these CIs also carried 37 Yr genes. Using these MQTLs, 385 candidate genes (CGs) were also identified. Out of these CGs, 241 encoded known R proteins and 120 showed differential expression due to stripe rust infection at the seedling stage; the remaining 24 CGs were common in the sense that they encoded R proteins as well as showed differential expression. The proteins encoded by CGs carried the following widely known domains: NBS-LRR domain, WRKY domains, ankyrin repeat domains, sugar transport domains, etc. Thirteen breeders' MQTLs (PVE > 20%) including four pairs of closely linked MQTLs are recommended for use in wheat molecular breeding, for future studies to understand the molecular mechanism of stripe rust resistance and for gene cloning.
Collapse
Grants
- BT/PR21024/AGIII/103/925/2016 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR21024/AGIII/103/925/2016 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR21024/AGIII/103/925/2016 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR21024/AGIII/103/925/2016 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR21024/AGIII/103/925/2016 Department of Biotechnology, Ministry of Science and Technology, India
- Indian National Science Academy
Collapse
Affiliation(s)
- Irfat Jan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Gautam Saripalli
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Kuldeep Kumar
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Anuj Kumar
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Rakhi Singh
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Ritu Batra
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Pradeep Kumar Sharma
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India.
| |
Collapse
|
73
|
Bilgili A, Çomaklı E. Evaluation of the relationship between root nutrients and root biomass in lands under different management practices. ENVIRONMENTAL MONITORING AND ASSESSMENT 2021; 193:799. [PMID: 34773518 DOI: 10.1007/s10661-021-09585-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
Abstract
Mastering ecological dynamics necessitates identifying the substance cycles in biomass. In terms of sustainable soil productivity, the nutrient content of below-ground biomass is just as significant as the above-ground biomass, which fluctuates depending on land use. Yet, there were limited studies on determining the quantity of plant nutrient stocks, particularly in the below-ground biomass, in rangeland, forest, and plantation areas coexisting in the same ecological zone. In this regard, it is expected that the findings of this study will contribute to the literature. For this purpose in mind, distinct samples were taken from three depth levels (0-10 cm, 10-20 cm, 20-30 cm) to determine root biomass and nutrient stocks of roots in neighboring rangeland, forest, and plantation areas, and roots were divided into diameter classes, and below-ground biomass amounts and nutritional contents of below-ground biomass were determined. According to the results obtained, the total root biomass in the rangelands is 8.02 Mg ha-1, total root biomass was 5.95 Mg ha-1 in forest areas, and in plantation areas, the total root biomass is 6.94 Mg ha-1. Root biomass in the 0-10 cm soil layer constituted 78% of the total biomass. Also, for all land uses, the highest below-ground biomass concentrations were observed for Al, Fe, K, Mg, and Ca. The amounts of Al, Fe, K and Mg in the below-ground biomass followed the sequence of rangeland, plantation, and forest from high to low. Nutrient stocks in below-ground biomass and the effects of increases in root biomass on plant growth should be evaluated by future studies.
Collapse
Affiliation(s)
- Adnan Bilgili
- Eastern Anatolia Forestry Research Institute, 25200, Erzurum, Turkey
| | - Emre Çomaklı
- Environmental Problems Research and Application Center, Atatürk University, 25240, Erzurum, Turkey.
| |
Collapse
|
74
|
Lin L, Sharma A, Yu Q. Recent amplification of microsatellite-associated miniature inverted-repeat transposable elements in the pineapple genome. BMC PLANT BIOLOGY 2021; 21:424. [PMID: 34537020 PMCID: PMC8449440 DOI: 10.1186/s12870-021-03194-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Miniature inverted-repeat transposable elements (MITEs) are non-autonomous DNA transposable elements that play important roles in genome organization and evolution. Genome-wide identification and characterization of MITEs provide essential information for understanding genome structure and evolution. RESULTS We performed genome-wide identification and characterization of MITEs in the pineapple genome. The top two MITE families, accounting for 29.39% of the total MITEs and 3.86% of the pineapple genome, have insertion preference in (TA) n dinucleotide microsatellite regions. We therefore named these MITEs A. comosus microsatellite-associated MITEs (Ac-mMITEs). The two Ac-mMITE families, Ac-mMITE-1 and Ac-mMITE-2, shared sequence similarity in the terminal inverted repeat (TIR) regions, suggesting that these two Ac-mMITE families might be derived from a common or closely related autonomous elements. The Ac-mMITEs are frequently clustered via adjacent insertions. Among the 21,994 full-length Ac-mMITEs, 46.1% of them were present in clusters. By analyzing the Ac-mMITEs without (TA) n microsatellite flanking sequences, we found that Ac-mMITEs were likely derived from Mutator-like DNA transposon. Ac-MITEs showed highly polymorphic insertion sites between cultivated pineapples and their wild relatives. To better understand the evolutionary history of Ac-mMITEs, we filtered and performed comparative analysis on the two distinct groups of Ac-mMITEs, microsatellite-targeting MITEs (mt-MITEs) that are flanked by dinucleotide microsatellites on both sides and mutator-like MITEs (ml-MITEs) that contain 9/10 bp TSDs. Epigenetic analysis revealed a lower level of host-induced silencing on the mt-MITEs in comparison to the ml-MITEs, which partially explained the significantly higher abundance of mt-MITEs in pineapple genome. The mt-MITEs and ml-MITEs exhibited differential insertion preference to gene-related regions and RNA-seq analysis revealed their differential influences on expression regulation of nearby genes. CONCLUSIONS Ac-mMITEs are the most abundant MITEs in the pineapple genome and they were likely derived from Mutator-like DNA transposon. Preferential insertion in (TA) n microsatellite regions of Ac-mMITEs occurred recently and is likely the result of damage-limiting strategy adapted by Ac-mMITEs during co-evolution with their host. Insertion in (TA) n microsatellite regions might also have promoted the amplification of mt-MITEs. In addition, mt-MITEs showed no or negligible impact on nearby gene expression, which may help them escape genome control and lead to their amplification.
Collapse
Affiliation(s)
- Lianyu Lin
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Anupma Sharma
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA
| | - Qingyi Yu
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA.
| |
Collapse
|
75
|
Liu L, Xie Z, Lu L, Qanmber G, Chen G, Li S, Guo M, Sun Z, Liu Z, Yang Z. Identification of BR biosynthesis genes in cotton reveals that GhCPD-3 restores BR biosynthesis and mediates plant growth and development. PLANTA 2021; 254:75. [PMID: 34533620 DOI: 10.1007/s00425-021-03727-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/08/2021] [Indexed: 06/13/2023]
Abstract
Brassinosteroid (BR) synthesis genes in different cotton species was comprehensively identified, and the participation of GhCPD-3 in the BR synthesis signaling pathway for regulating plant development was verified. Brassinosteroid is a natural steroidal phytohormone that plays fundamental roles in plant growth and development. In cotton, detailed characterization and functional validation of BR biosynthesis genes remain rare. Here, 16, 8 and 9 BR biosynthesis genes were identified in Gossypium hirsutum, Gossypium raimondii and Gossypium arboreum, respectively, and their phylogenetic relationships, gene structures, conserved motifs of the encoded proteins, chromosomal locations were determined and a synteny analysis was performed. Gossypium hirsutum and Arabidopsis BR biosynthesis genes closely clustered in the phylogenetic tree and fragment duplication was likely the primary cause promoting gene family expansion in G. hirsutum. Gene Ontology (GO) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis showed their relevance as BR biosynthesis genes. GhCPD-3 was highly expressed in roots and stems and the loci of single nucleotide polymorphisms (SNPs) were significantly associated with these traits.Ectopic overexpression of GhCPD-3 in the cpd91 Arabidopsis mutant rescued the mutant phenotype by increasing plant height and leaf size in comparison to those of cpd91 and WT plants. Moreover, overexpressed GhCPD-3 in cpd91 mutants showed greater hypocotyl and root lengths than those of cpd91 and WT plants under light and dark conditions, respectively, indicating that BR actively promotes hypocotyl and root growth. Similar to CPD (CONSTITUTIVE PHOTOMORPHOGENIC DWARF), GhCPD-3 restores BR biosynthesis thereby mediating plant growth and development.
Collapse
Affiliation(s)
- Le Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Zongming Xie
- Xinjiang Production and Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Biotechnology Research Institute of Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, 832000, Xinjiang, China
| | - Lili Lu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Ghulam Qanmber
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Guoquan Chen
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Shengdong Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Mengzhen Guo
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Zhuojing Sun
- Development Center for Science and Technology, Ministry of Agriculture and Rural Affairs, Beijing, 100122, China
| | - Zhao Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| | - Zuoren Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| |
Collapse
|
76
|
Enzymatic characterization of the saliva of the eriophyid mite, Aceria pongamiae Keifer1966 (Acari: Eriophyidae) and the bacterial endobiome of the galls induced on Pongamia pinnata (L.) Pierre (Fabaceae). Naturwissenschaften 2021; 108:33. [PMID: 34302542 DOI: 10.1007/s00114-021-01743-z] [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: 04/22/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 10/20/2022]
Abstract
Galls, like other regular plant organs, possess their own histological and physiological features. A high degree of specificity is maintained between the host and the inducer, and hence gall morphogenesis is highly conserved and would help trace gall lineages and cell fate. The present study highlights the induction and subsequent development of leaf galls on the Indian Beech tree, Pongamia pinnata (L) Pierre (Fabaceae), mediated through the active participation of a gall-inducing species of eriophyid mite, Aceria pongamiae Keifer and gall-associated bacterial endobiome. The saliva of A. pongamiae and selected strains of gall-associated bacterial endobiome were characterized in part during the study. Three strains of Staphylococcus arlettae (PGP1-3) and one strain of Bacillus flexus (PGP4) were identified from the leaf galls through 16S rDNA sequencing. The mite saliva displayed tryptophanase activity, and the bacterial strains showed differential enzyme activities (protease, amylase, cellulase, DNAse, pectinase, tryptophanase, and catalase). All four strains of bacterial endobiome exhibited unique metal tolerance as well as pH and temperature regulating activity. Evaluation of the potential role of the mite saliva and the gall associated bacterial endobiome in gallogenesis was done by monitoring the plant growth-promoting activity of the salivary extract and the isolated bacterial strains through in vitro seed (Vigna radiata) germination assay. Salivary extract of the mite showed the highest rate of plant growth-promoting activity compared with that of the isolated strains of bacterial endobiome. The present study forms the first attempt that illustrates the characteristic features of the saliva of the gall inducer and the gall associated bacterial endobiome. Based on the results of the current study, we suggest that eriophyid mite saliva and the gall-associated microbes play significant roles in the induction of cecidia.
Collapse
|