1
|
Vasisth P, Singh N, Limbalkar OM, Sharma M, Dhanasekaran G, Meena ML, Jain P, Jaiswal S, Iquebal MA, Watts A, Gaikwad KB, Singh R. Introgression of Heterotic Genomic Segments from Brassica carinata into Brassica juncea for Enhancing Productivity. PLANTS (BASEL, SWITZERLAND) 2023; 12:1677. [PMID: 37111905 PMCID: PMC10146992 DOI: 10.3390/plants12081677] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/18/2023] [Accepted: 04/11/2023] [Indexed: 06/19/2023]
Abstract
Interspecific hybridization resulted in the creation of B. juncea introgression lines (ILs) generated from B. carinata with increased productivity and adaptability. Forty ILs were crossed with their respective B. juncea recipient parents to generate introgression line hybrids (ILHs) and the common tester (SEJ 8) was used to generate test hybrids (THs). Mid-parent heterosis in ILHs and standard heterosis in THs were calculated for eight yield and yield-related traits. Heterotic genomic regions were dissected using ten ILs with significant mid-parent heterosis in ILHs and standard heterosis in THs for seed yield. A high level of heterosis for seed yield was contributed by 1000 seed weight (13.48%) in D31_ILHs and by total siliquae/plant (14.01%) and siliqua length (10.56%) in PM30_ILHs. The heterotic ILs of DRMRIJ 31 and Pusa Mustard 30 were examined using polymorphic SNPs between the parents, and a total of 254 and 335 introgressed heterotic segments were identified, respectively. This investigation discovered potential genes, viz., PUB10, glutathione S transferase, TT4, SGT, FLA3, AP2/ERF, SANT4, MYB, and UDP-glucosyl transferase 73B3 that were previously reported to regulate yield-related traits. The heterozygosity of the FLA3 gene significantly improved siliqua length and seeds per siliqua in ILHs of Pusa Mustard 30. This research proved that interspecific hybridization is an effective means of increasing the diversity of cultivated species by introducing new genetic variants and improving the level of heterosis.
Collapse
Affiliation(s)
- Prashant Vasisth
- Division of Genetics, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Naveen Singh
- Division of Genetics, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Omkar Maharudra Limbalkar
- Division of Genetics, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Mohit Sharma
- Division of Genetics, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Gokulan Dhanasekaran
- Division of Genetics, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Mohan Lal Meena
- Division of Genetics, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Priyanka Jain
- Division of Agricultural Bioinformatics, Indian Council of Agricultural Research-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, Indian Council of Agricultural Research-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, Indian Council of Agricultural Research-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Anshul Watts
- Indian Council of Agricultural Research-National Institute of Plant Biotechnology, New Delhi 110012, India
| | - Kiran B. Gaikwad
- Division of Genetics, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Rajendra Singh
- Division of Genetics, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi 110012, India
| |
Collapse
|
2
|
Agrawal N, Gupta M, Banga SS, Heslop-Harrison JS(P. Identification of Chromosomes and Chromosome Rearrangements in Crop Brassicas and Raphanus sativus: A Cytogenetic Toolkit Using Synthesized Massive Oligonucleotide Libraries. FRONTIERS IN PLANT SCIENCE 2020; 11:598039. [PMID: 33414797 PMCID: PMC7783396 DOI: 10.3389/fpls.2020.598039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 11/30/2020] [Indexed: 05/10/2023]
Abstract
Crop brassicas include three diploid [Brassica rapa (AA; 2n = 2x = 16), B. nigra (BB; 2n = 2x = 18), and B. oleracea (CC; 2n = 2x = 20)] and three derived allotetraploid species. It is difficult to distinguish Brassica chromosomes as they are small and morphologically similar. We aimed to develop a genome-sequence based cytogenetic toolkit for reproducible identification of Brassica chromosomes and their structural variations. A bioinformatic pipeline was used to extract repeat-free sequences from the whole genome assembly of B. rapa. Identified sequences were subsequently used to develop four c. 47-mer oligonucleotide libraries comprising 27,100, 11,084, 9,291, and 16,312 oligonucleotides. We selected these oligonucleotides after removing repeats from 18 identified sites (500-1,000 kb) with 1,997-5,420 oligonucleotides localized at each site in B. rapa. For one set of probes, a new method for amplification or immortalization of the library is described. oligonucleotide probes produced specific and reproducible in situ hybridization patterns for all chromosomes belonging to A, B, C, and R (Raphanus sativus) genomes. The probes were able to identify structural changes between the genomes, including translocations, fusions, and deletions. Furthermore, the probes were able to identify a structural translocation between a pak choi and turnip cultivar of B. rapa. Overall, the comparative chromosomal mapping helps understand the role of chromosome structural changes during genome evolution and speciation in the family Brassicaceae. The probes can also be used to identify chromosomes in aneuploids such as addition lines used for gene mapping, and to track transfer of chromosomes in hybridization and breeding programs.
Collapse
Affiliation(s)
- Neha Agrawal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Mehak Gupta
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Surinder S. Banga
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - JS (Pat) Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| |
Collapse
|
3
|
Balakrishnan D, Surapaneni M, Mesapogu S, Neelamraju S. Development and use of chromosome segment substitution lines as a genetic resource for crop improvement. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1-25. [PMID: 30483819 DOI: 10.1007/s00122-018-3219-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 10/24/2018] [Indexed: 05/27/2023]
Abstract
CSSLs are a complete library of introgression lines with chromosomal segments of usually a distant genotype in an adapted background and are valuable genetic resources for basic and applied research on improvement of complex traits. Chromosome segment substitution lines (CSSLs) are genetic stocks representing the complete genome of any genotype in the background of a cultivar as overlapping segments. Ideally, each CSSL has a single chromosome segment from the donor with a maximum recurrent parent genome recovered in the background. CSSL development program requires population-wide backcross breeding and genome-wide marker-assisted selection followed by selfing. Each line in a CSSL library has a specific marker-defined large donor segment. CSSLs are evaluated for any target phenotype to identify lines significantly different from the parental line. These CSSLs are then used to map quantitative trait loci (QTLs) or causal genes. CSSLs are valuable prebreeding tools for broadening the genetic base of existing cultivars and harnessing the genetic diversity from the wild- and distant-related species. These are resources for genetic map construction, mapping QTLs, genes or gene interactions and their functional analysis for crop improvement. In the last two decades, the utility of CSSLs in identification of novel genomic regions and QTL hot spots influencing a wide range of traits has been well demonstrated in food and commercial crops. This review presents an overview of how CSSLs are developed, their status in major crops and their use in genomic studies and gene discovery.
Collapse
Affiliation(s)
- Divya Balakrishnan
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Malathi Surapaneni
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Sukumar Mesapogu
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Sarla Neelamraju
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India.
| |
Collapse
|
4
|
Zhu B, Xiang Y, Zeng P, Cai B, Huang X, Ge X, Weng Q, Li Z. Genome-Wide Gene Expression Disturbance by Single A1/C1 Chromosome Substitution in Brassica rapa Restituted From Natural B. napus. FRONTIERS IN PLANT SCIENCE 2018; 9:377. [PMID: 29616075 PMCID: PMC5870043 DOI: 10.3389/fpls.2018.00377] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Accepted: 03/07/2018] [Indexed: 05/29/2023]
Abstract
Alien chromosome substitution (CS) lines are treated as vital germplasms for breeding and genetic mapping. Previously, a whole set of nine Brassica rapa-oleracea monosonic alien addition lines (MAALs, C1-C9) was established in the background of natural B. napus genotype "Oro," after the restituted B. rapa (RBR) for Oro was realized. Herein, a monosomic substitution line with one alien C1 chromosome (Cs1) in the RBR complement was selected in the progenies of MAAL C1 and RBR, by the PCR amplification of specific gene markers and fluorescence in situ hybridization. Cs1 exhibited the whole plant morphology similar to RBR except for the defective stamens without fertile pollen grains, but it produced some seeds and progeny plants carrying the C1 chromosome at high rate besides those without the alien chromosome after pollinated by RBR. The viability of the substitution and its progeny for the RBR diploid further elucidated the functional compensation between the chromosome pairs with high homoeology. To reveal the impact of such aneuploidy on genome-wide gene expression, the transcriptomes of MAAL C1, Cs1 and euploid RBR were analyzed. Compared to RBR, Cs1 had sharply reduced gene expression level across chromosome A1, demonstrating the loss of one copy of A1 chromosome. Both additional chromosome C1 in MAAL and substitutional chromosome C1 in Cs1 caused not only cis-effect but also prevalent trans-effect differentially expressed genes. A dominant gene dosage effects prevailed among low expressed genes across chromosome A1 in Cs1, and moreover, dosage effects for some genes potentially contributed to the phenotype deviations. Our results provided novel insights into the transcriptomic perturbation and gene dosage effects on phenotype in CS related to one naturally evolved allopolyploid.
Collapse
Affiliation(s)
- Bin Zhu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yang Xiang
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Pan Zeng
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Bowei Cai
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaolong Huang
- Key Laboratory of Plant Physiology and Development Regulation, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Xianhong Ge
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qingbei Weng
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Zaiyun Li
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
5
|
Prohens J, Gramazio P, Plazas M, Dempewolf H, Kilian B, Díez MJ, Fita A, Herraiz FJ, Rodríguez-Burruezo A, Soler S, Knapp S, Vilanova S. Introgressiomics: a new approach for using crop wild relatives in breeding for adaptation to climate change. EUPHYTICA 2017; 213:158. [PMID: 0 DOI: 10.1007/s10681-017-1938-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 06/23/2017] [Indexed: 05/29/2023]
|
6
|
Cytogenetic and Molecular Characterization of B-Genome Introgression Lines of Brassica napus L. G3-GENES GENOMES GENETICS 2017; 7:77-86. [PMID: 27821632 PMCID: PMC5217125 DOI: 10.1534/g3.116.036442] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Brassica napus introgression lines (ILs), having B-genome segments from B. carinata, were assessed genetically for extent of introgression and phenotypically for siliqua shatter resistance. Introgression lines had 7-9% higher DNA content, were meiotically stable, and had almost normal pollen fertility/seed set. Segment introgressions were confirmed by fluorescent genomic in situ hybridization (fl-GISH), SSR analyses, and SNP studies. Genotyping with 48 B-genome specific SSRs detected substitutions from B3, B4, B6, and B7 chromosomes on 39 of the 69 ILs whereas SNP genotyping detected a total of 23 B-segments (≥3 Mb) from B4, B6, and B7 introgressed into 10 of the 19 (C1, C2, C3, C5, C6, C8, C9, A3, A9, A10) chromosomes in 17 ILs. The size of substitutions varied from 3.0 Mb on chromosome A9 (IL59) to 42.44 Mb on chromosome C2 (IL54), ranging from 7 to 83% of the recipient chromosome. Average siliqua strength in ILs was observed to be higher than that of B. napus parents (2.2-6.0 vs. 1.9-4.0 mJ) while siliqua strength in some of the lines was almost equal to that of the donor parent B. carinata (6.0 vs.7.2 mJ). These ILs, with large chunks of substituted B-genome, can prove to be a useful prebreeding resource for germplasm enhancement in B. napus, especially for siliqua shatter resistance.
Collapse
|