1
|
Zhang W, Wang H, Zhang T, Fang X, Liu M, Xiao H. Geographic-genomic and geographic-phenotypic differentiation of the Aquilegia viridiflora complex. HORTICULTURE RESEARCH 2023; 10:uhad041. [PMID: 37159802 PMCID: PMC10163360 DOI: 10.1093/hr/uhad041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 03/05/2023] [Indexed: 05/11/2023]
Abstract
How species diverge into different lineages is a central issue in evolutionary biology. Despite the increasing evidence indicating that such divergences do not need geographic isolation, the correlation between lineage divergence and the adaptive ecological divergence of phenotype corresponding to distribution is still unknown. In addition, gene flow has been widely detected during and through such diverging processes. We used one widely distributed Aquilegia viridiflora complex as a model system to examine genomic differentiation and corresponding phenotypic variations along geographic gradients. Our phenotypic analyses of 20 populations from northwest to northeast China identified two phenotypic groups along the geographic cline. All examined traits are distinct from each other, although a few intermediate individuals occur in their contacting regions. We further sequenced the genomes of representative individuals of each population. However, four distinct genetic lineages were detected based on nuclear genomes. In particular, we recovered numerous genetic hybrids in the contact regions of four lineages. Gene flow is widespread and continuous between four lineages but much higher between contacting lineages than geographically isolated lineages. Gene flow and natural selection might result in inconsistency between heredity and phenotype. Moreover, many genes with fast lineage-specific mutations were identified to be involved in local adaptation. Our results suggest that both geographic isolation and local selection exerted by the environment and pollinators may together create geographic distributions of phenotypic variations as well as the underlying genomic divergences in numerous lineages.
Collapse
Affiliation(s)
- Wei Zhang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, College of Life Sciences, Northeast Normal University, Changchun 130024, China
| | | | - Tengjiao Zhang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, College of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Xiaoxue Fang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, College of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Meiying Liu
- Key Laboratory of Molecular Epigenetics of Ministry of Education, College of Life Sciences, Northeast Normal University, Changchun 130024, China
| | | |
Collapse
|
2
|
Ma Z, Du R, Xie J, Sun D, Fang H, Jiang L, Cen H. Phenotyping of Silique Morphology in Oilseed Rape Using Skeletonization with Hierarchical Segmentation. PLANT PHENOMICS (WASHINGTON, D.C.) 2023; 5:0027. [PMID: 36939450 PMCID: PMC10017417 DOI: 10.34133/plantphenomics.0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Silique morphology is an important trait that determines the yield output of oilseed rape (Brassica napus L.). Segmenting siliques and quantifying traits are challenging because of the complicated structure of an oilseed rape plant at the reproductive stage. This study aims to develop an accurate method in which a skeletonization algorithm was combined with the hierarchical segmentation (SHS) algorithm to separate siliques from the whole plant using 3-dimensional (3D) point clouds. We combined the L1-median skeleton with the random sample consensus for iteratively extracting skeleton points and optimized the skeleton based on information such as distance, angle, and direction from neighborhood points. Density-based spatial clustering of applications with noise and weighted unidirectional graph were used to achieve hierarchical segmentation of siliques. Using the SHS, we quantified the silique number (SN), silique length (SL), and silique volume (SV) automatically based on the geometric rules. The proposed method was tested with the oilseed rape plants at the mature stage grown in a greenhouse and field. We found that our method showed good performance in silique segmentation and phenotypic extraction with R 2 values of 0.922 and 0.934 for SN and total SL, respectively. Additionally, SN, total SL, and total SV had the statistical significance of correlations with the yield of a plant, with R values of 0.935, 0.916, and 0.897, respectively. Overall, the SHS algorithm is accurate, efficient, and robust for the segmentation of siliques and extraction of silique morphological parameters, which is promising for high-throughput silique phenotyping in oilseed rape breeding.
Collapse
Affiliation(s)
- Zhihong Ma
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, P.R. China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, P.R. China
| | - Ruiming Du
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, P.R. China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, P.R. China
| | - Jiayang Xie
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, P.R. China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, P.R. China
| | - Dawei Sun
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, P.R. China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, P.R. China
| | - Hui Fang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, P.R. China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, P.R. China
| | - Lixi Jiang
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, P.R. China
| | - Haiyan Cen
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, P.R. China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, P.R. China
| |
Collapse
|
3
|
Dhaka N, Sharma R. MicroRNA-mediated regulation of agronomically important seed traits: a treasure trove with shades of grey! Crit Rev Biotechnol 2021; 41:594-608. [PMID: 33682533 DOI: 10.1080/07388551.2021.1873238] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Seed development is an intricate process with multiple levels of regulation. MicroRNAs (miRNAs) have emerged as one of the crucial components of molecular networks underlying agronomically important seed traits in diverse plant species. In fact, loss of function of the genes regulating miRNA biogenesis also exhibits defects in seed development. A total of 21 different miRNAs have experimentally been shown to regulate seed size, nutritional content, vigor, and shattering, and have been reviewed here. The mechanism details of the associated regulatory cascades mediated through transcriptional regulators, phytohormones, basic metabolic machinery, and secondary siRNAs are elaborated. Co-localization of miRNAs and their target regions with seed-related QTLs provides new avenues for engineering these traits using conventional breeding programs or biotechnological interventions. While global analysis of miRNAs using small RNA sequencing studies are expanding the repertoire of candidate miRNAs, recent revelations on their inheritance, transport, and mechanism of action would be instrumental in designing better strategies for optimizing agronomically relevant seed traits.
Collapse
Affiliation(s)
- Namrata Dhaka
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Haryana, India.,Crop Genetics and Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rita Sharma
- Crop Genetics and Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| |
Collapse
|
4
|
Wang T, Xiong B, Tan L, Yang Y, Zhang Y, Ma M, Xu Y, Liao L, Sun G, Liang D, Xia H, Zhang X, Wang Z, Wang J. Effects of interstocks on growth and photosynthetic characteristics in 'Yuanxiaochun' Citrus seedlings. FUNCTIONAL PLANT BIOLOGY : FPB 2020; 47:977-987. [PMID: 32645281 DOI: 10.1071/fp20079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/23/2020] [Indexed: 06/11/2023]
Abstract
To obtain the compatibility of interstocks crossing with 'Yuanxiaochun', we performed a comparative analysis with five interstocks. From the 60th to 240th day after grafting, there was a significant difference between different treatments. All the new shoot/interstock diameter ratios were <1, indicating that there was no obvious phenomenon of small feet in 'Yuanxiaochun' seedlings of five kinds of interstocks. The density of 'Yuanxiaochun' was significantly different. Chl a, Chl b, T-Chl content of 'Shiranuhi', 'Harumi', 'Tarocco' changed greatly from the 90th to 120th day after grafting. The intercellular CO2 concentration (Ci) of 'Shiranuhi' was significantly higher than the other interstocks. In addition, when 'Yuanxiaochun' was grafted onto 'Shiranuhi', net photosynthetic rate (Pn), stomatal conductance (gs) and tanspiration rate (Tr) were higher. When 'Harumi' were used as the interstocks of 'Yuanxiaochun', the light saturation point (LSP) value was larger, which was conducive to the utilisation of strong light. Moreover, the value of LSP-LCP (LCP, light compensation point) of 'Harumi' and 'Tarocco' were significantly higher than the other three interstocks. The apparent quantum efficiency (AQE), RuBP maximum regeneration rate (Jmax) and maximum carboxylation efficiency of Rubisco (Vcmax) value of 'Shiranuhi' was significantly lower than that of 'Ponkan'. The CO2 compensation point (CCP) of 'Harumi' interstock was lower, but the CO2 saturation point (CSP) of 'Tarocco' interstock was higher than those of other interstocks respectively. There was a small difference in initial fluorescence (F0) of different interstocks. The maximal photochemical efficiency of PSII in the dark (Fv/Fm) of 'Kumquat' was the lowest. In addition, Both Y(II) and ETR values of the 'Yuanxiaochun' leaves of 'Ponkan' interstock was the largest one. However, the non-photochemical quenching (qN) of 'Ponkan' was significantly lower, and that of 'Tarocco' interstock was the highest one. Interstocks have different effect on the growth and development, photosynthetic characteristics related to physiological characteristics of 'Yuanxiaochun' trees. 'Ponkan' and 'Kumquat' as the interstock of 'Yuanxiaochun' was more conducive to the rapid accumulation of photosynthetic products for normal vegetative and reproductive growth of plants.
Collapse
Affiliation(s)
- Tie Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Bo Xiong
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Liping Tan
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Youting Yang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yue Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Mengmeng Ma
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yinghuan Xu
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Ling Liao
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Guochao Sun
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Dong Liang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Hui Xia
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xiaoai Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Zhihui Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China; and Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China; and Corresponding authors. ;
| | - Jun Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China; and Corresponding authors. ;
| |
Collapse
|
5
|
Raman H, Raman R, McVittie B, Borg L, Diffey S, Singh Yadav A, Balasubramanian S, Farquhar G. Genetic and physiological bases for variation in water use efficiency in canola. Food Energy Secur 2020. [DOI: 10.1002/fes3.237] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Harsh Raman
- NSW Department of Primary Industries Wagga Wagga Agricultural Institute Wagga Wagga NSW Australia
| | - Rosy Raman
- NSW Department of Primary Industries Wagga Wagga Agricultural Institute Wagga Wagga NSW Australia
| | - Brett McVittie
- NSW Department of Primary Industries Wagga Wagga Agricultural Institute Wagga Wagga NSW Australia
| | - Lauren Borg
- University of Wollongong Wollongong NSW Australia
| | | | | | | | - Graham Farquhar
- Research School of Biology Australian National University Canberra ACT Australia
| |
Collapse
|
6
|
Raman H, Raman R, Qiu Y, Yadav AS, Sureshkumar S, Borg L, Rohan M, Wheeler D, Owen O, Menz I, Balasubramanian S. GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola. BMC Genomics 2019; 20:636. [PMID: 31387521 PMCID: PMC6685183 DOI: 10.1186/s12864-019-5964-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 07/09/2019] [Indexed: 12/20/2022] Open
Abstract
Background Transition to flowering at the right time is critical for local adaptation and to maximize grain yield in crops. Canola is an important oilseed crop with extensive variation in flowering time among varieties. However, our understanding of underlying genes and their role in canola productivity is limited. Results We report our analyses of a diverse GWAS panel (300–368 accessions) of canola and identify SNPs that are significantly associated with variation in flowering time and response to photoperiod across multiple locations. We show that several of these associations map in the vicinity of FLOWERING LOCUS T (FT) paralogs and its known transcriptional regulators. Complementary QTL and eQTL mapping studies, conducted in an Australian doubled haploid population, also detected consistent genomic regions close to the FT paralogs associated with flowering time and yield-related traits. FT sequences vary between accessions. Expression levels of FT in plants grown in field (or under controlled environment cabinets) correlated with flowering time. We show that markers linked to the FT paralogs display association with variation in multiple traits including flowering time, plant emergence, shoot biomass and grain yield. Conclusions Our findings suggest that FT paralogs not only control flowering time but also modulate yield-related productivity traits in canola. Electronic supplementary material The online version of this article (10.1186/s12864-019-5964-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Harsh Raman
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia.
| | - Rosy Raman
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia
| | - Yu Qiu
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia
| | - Avilash Singh Yadav
- School of Biological Sciences, Monash University, Clayton, VIC3800, Australia
| | - Sridevi Sureshkumar
- School of Biological Sciences, Monash University, Clayton, VIC3800, Australia
| | - Lauren Borg
- Centre for Bioinformatics and Biometrics, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Maheswaran Rohan
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia
| | - David Wheeler
- NSW Department of Primary Industries, Orange Agricultural Institute, Orange, NSW, 2800, Australia
| | - Oliver Owen
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia
| | - Ian Menz
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia
| | | |
Collapse
|