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Sari D. Identification of Insertion and Deletion (InDel) Markers for Chickpea ( Cicer arietinum L.) Based on Double-Digest Restriction Site-Associated DNA Sequencing. PLANTS (BASEL, SWITZERLAND) 2024; 13:2530. [PMID: 39274014 PMCID: PMC11397535 DOI: 10.3390/plants13172530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Revised: 09/03/2024] [Accepted: 09/04/2024] [Indexed: 09/16/2024]
Abstract
Enhancing the marker repository and the development of breeder-friendly markers in chickpeas is important in relation to chickpea genomics-assisted breeding applications. Insertion-deletion (InDel) markers are widely distributed across genomes and easily observed with specifically designed primers, leading to less time, cost, and labor requirements. In light of this, the present study focused on the identification and development of InDel markers through the use of double-digest restriction site-associated DNA sequencing (ddRADSeq) data from 20 chickpea accessions. Bioinformatic analysis identified 20,700 InDel sites, including 15,031 (72.61%) deletions and 5669 (27.39%) insertions, among the chickpea accessions. The InDel markers ranged from 1 to 25 bp in length, while single-nucleotide-length InDel markers were found to represent the majority of the InDel sites and account for 79% of the total InDel markers. However, we focused on InDel markers wherein the length was greater than a single nucleotide to avoid any read or alignment errors. Among all of the InDel markers, 96.1% were less than 10 bp, 3.6% were between 10 and 20 bp, and 0.3% were more than 20 bp in length. We examined the InDel markers that were 10 bp and longer for the development of InDel markers based on a consideration of the genomic distribution and low-cost genotyping with agarose gels. A total of 29 InDel regions were selected, and primers were successfully designed to evaluate their efficiency. Annotation analysis of the InDel markers revealed them to be found with the highest frequency in the intergenic regions (82.76%), followed by the introns (6.90%), coding sequences (6.90%), and exons (3.45%). Genetic diversity analysis demonstrated that the polymorphic information content of the markers varied from 0.09 to 0.37, with an average of 0.20. Taken together, these results showed the efficiency of InDel marker development for chickpea genetic and genomic studies using the ddRADSeq method. The identified markers might prove valuable for chickpea breeders.
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Affiliation(s)
- Duygu Sari
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, 07070 Antalya, Turkey
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Redelings BD, Holmes I, Lunter G, Pupko T, Anisimova M. Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications. Mol Biol Evol 2024; 41:msae177. [PMID: 39172750 PMCID: PMC11385596 DOI: 10.1093/molbev/msae177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 07/02/2024] [Accepted: 07/09/2024] [Indexed: 08/24/2024] Open
Abstract
Insertions and deletions constitute the second most important source of natural genomic variation. Insertions and deletions make up to 25% of genomic variants in humans and are involved in complex evolutionary processes including genomic rearrangements, adaptation, and speciation. Recent advances in long-read sequencing technologies allow detailed inference of insertions and deletion variation in species and populations. Yet, despite their importance, evolutionary studies have traditionally ignored or mishandled insertions and deletions due to a lack of comprehensive methodologies and statistical models of insertions and deletion dynamics. Here, we discuss methods for describing insertions and deletion variation and modeling insertions and deletions over evolutionary time. We provide practical advice for tackling insertions and deletions in genomic sequences and illustrate our discussion with examples of insertions and deletion-induced effects in human and other natural populations and their contribution to evolutionary processes. We outline promising directions for future developments in statistical methodologies that would allow researchers to analyze insertions and deletion variation and their effects in large genomic data sets and to incorporate insertions and deletions in evolutionary inference.
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Affiliation(s)
| | - Ian Holmes
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA
| | - Gerton Lunter
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen 9713 GZ, The Netherlands
| | - Tal Pupko
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Maria Anisimova
- Institute of Computational Life Sciences, Zurich University of Applied Sciences, Wädenswil, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Shao L, Qiao P, Wang J, Peng Y, Wang Y, Dong W, Li J. Comparative analysis of jujube and sour jujube gave insight into their difference in genetic diversity and suitable habitat. Front Genet 2024; 15:1322285. [PMID: 38380425 PMCID: PMC10878421 DOI: 10.3389/fgene.2024.1322285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/16/2024] [Indexed: 02/22/2024] Open
Abstract
Jujube (Ziziphus jujuba var. jujuba Mill.) and sour jujube (Z. jujuba var. spinosa (Bunge) Hu ex H.F.Chow.) are economically, nutritionally, and ecologically significant members of the Rhamnaceae family. Despite their importance, insufficient research on their genetics and habitats has impeded effective conservation and utilization. To address this knowledge gap, we conducted plastome sequencing, integrated distribution data from China, and assessed genetic diversity and suitable habitat. The plastomes of both species exhibited high conservation and low genetic diversity. A new-found 23 bp species-specific Indel in the petL-petG enabled us to develop a rapid Indel-based identification marker for species discrimination. Phylogenetic analysis and dating illuminated their genetic relationship, showing speciation occurred 6.9 million years ago, in a period of dramatic global temperature fluctuations. Substantial variations in suitable climatic conditions were observed, with the mean temperature of the coldest quarter as the primary factor influencing distributions (-3.16°C-12.73°C for jujube and -5.79°C to 4.11°C for sour jujube, suitability exceeding 0.6). Consequently, distinct conservation strategies are warranted due to differences in suitable habitats, with jujube having a broader distribution and sour jujube concentrated in Northern China. In conclusion, disparate habitats and climatic factors necessitate tailored conservation approaches. Comparing genetic diversity and developing rapid species-specific primers will further enhance the sustainable utilization of these valuable species.
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Affiliation(s)
- Lingzhi Shao
- School of Biology and Food Science, Hebei Normal University for Nationalities, Chengde, China
| | - Ping Qiao
- Dexing Research and Training Center of Chinese Medical Sciences, China Academy of Chinese Medical Sciences, Dexing, China
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jingyi Wang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yanfang Peng
- School of Biology and Food Science, Hebei Normal University for Nationalities, Chengde, China
| | - Yiheng Wang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wenpan Dong
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jie Li
- School of Biology and Food Science, Hebei Normal University for Nationalities, Chengde, China
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Zhou Q, Hu H, Yang Y, Kang Y, Lan X, Wu X, Guo Z, Pan C. Insertion/deletion (Indel) variant of the goat RORA gene is associated with growth traits. Anim Biotechnol 2023; 34:2175-2182. [PMID: 35622416 DOI: 10.1080/10495398.2022.2078980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
RAR related orphan receptor A (RORA), which encodes the retinoid-acid-related orphan receptor alpha (RORα), is a clock gene found in skeletal muscle. Several studies have shown that RORα plays an important role in bone formation, suggesting that RORA gene may take part in the regulation of growth and development. The purpose of this research is to study the insertion/deletion (indel) variations of the RORA gene and investigate the relationship with the growth traits of Shaanbei white cashmere (SBWC) goats. Herein, the current study identified that the P4-11-bp and P11-28-bp deletion sites are polymorphic among 12 pairs of primers within the RORA gene in the SBWC goats (n = 641). Moreover, the P11-28-bp deletion locus was significantly related to the body height (p = 0.046), height at hip cross (p = 0.012), and body length (p = 0.003). Both of P4-11-bp and P11-28-bp indels showed the moderate genetic diversity (0.25
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Affiliation(s)
- Qian Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Huina Hu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuta Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuxin Kang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xianfeng Wu
- Institute of Animal Husbandry and Veterinary, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Zhengang Guo
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
- Animal Husbandry and Veterinary Science Institute of Bijie city, Bijie, Guizhou, China
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
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Li Y, Luo X, Peng X, Jin Y, Tan H, Wu L, Li J, Pei Y, Xu X, Zhang W. Development of SNP and InDel markers by genome resequencing and transcriptome sequencing in radish (Raphanus sativus L.). BMC Genomics 2023; 24:445. [PMID: 37553577 PMCID: PMC10408230 DOI: 10.1186/s12864-023-09528-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 07/21/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND Single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) are the most abundant genetic variations and widely distribute across the genomes in plant. Development of SNP and InDel markers is a valuable tool for genetics and genomic research in radish (Raphanus sativus L.). RESULTS In this study, a total of 366,679 single nucleotide polymorphisms (SNPs) and 97,973 insertion-deletion (InDel) markers were identified based on genome resequencing between 'YZH' and 'XHT'. In all, 53,343 SNPs and 4,257 InDels were detected in two cultivars by transcriptome sequencing. Among the InDel variations, 85 genomic and 15 transcriptomic InDels were newly developed and validated PCR. The 100 polymorphic InDels markers generated 207 alleles among 200 Chinese radish germplasm, with an average 2.07 of the number of alleles (Na) and with an average 0.33 of the polymorphism information content (PIC). Population structure and phylogenetic relationship revealed that the radish cultivars from northern China were clustered together and the southwest China cultivars were clustered together. RNA-Seq analysis revealed that 11,003 differentially expressed genes (DEGs) were identified between the two cultivars, of which 5,020 were upregulated and 5,983 were downregulated. In total, 145 flowering time-related DGEs were detected, most of which were involved in flowering time integrator, circadian clock/photoperiod autonomous, and vernalization pathways. In flowering time-related DGEs region, 150 transcriptomic SNPs and 9 InDels were obtained. CONCLUSIONS The large amount of SNPs and InDels identified in this study will provide a valuable marker resource for radish genetic and genomic studies. The SNPs and InDels within flowering time-related DGEs provide fundamental insight into for dissecting molecular mechanism of bolting and flowering in radish.
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Affiliation(s)
- Yadong Li
- College of Agriculture, Guizhou University, Guiyang, 550003 China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003 China
| | - Xiaobo Luo
- Guizhou Province Academy of Agricultural Sciences, Guizhou Institute of Biotechnology, Guiyang, 550003 China
| | - Xiao Peng
- College of Agriculture, Guizhou University, Guiyang, 550003 China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003 China
| | - Yueyue Jin
- College of Agriculture, Guizhou University, Guiyang, 550003 China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003 China
| | - Huping Tan
- College of Agriculture, Guizhou University, Guiyang, 550003 China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003 China
| | - Linjun Wu
- College of Agriculture, Guizhou University, Guiyang, 550003 China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003 China
| | - Jingwei Li
- College of Agriculture, Guizhou University, Guiyang, 550003 China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003 China
| | - Yun Pei
- College of Agriculture, Guizhou University, Guiyang, 550003 China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003 China
| | - Xiuhong Xu
- College of Agriculture, Guizhou University, Guiyang, 550003 China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003 China
| | - Wanping Zhang
- College of Agriculture, Guizhou University, Guiyang, 550003 China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003 China
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Barbosa CFC, Asunto JC, Koh RBL, Santos DMC, Zhang D, Cao EP, Galvez LC. Genome-Wide SNP and Indel Discovery in Abaca ( Musa textilis Née) and among Other Musa spp. for Abaca Genetic Resources Management. Curr Issues Mol Biol 2023; 45:5776-5797. [PMID: 37504281 PMCID: PMC10377871 DOI: 10.3390/cimb45070365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/29/2023] Open
Abstract
Abaca (Musa textilis Née) is an economically important fiber crop in the Philippines. Its economic potential, however, is hampered by biotic and abiotic stresses, which are exacerbated by insufficient genomic resources for varietal identification vital for crop improvement. To address these gaps, this study aimed to discover genome-wide polymorphisms among abaca cultivars and other Musa species and analyze their potential as genetic marker resources. This was achieved through whole-genome Illumina resequencing of abaca cultivars and variant calling using BCFtools, followed by genetic diversity and phylogenetic analyses. A total of 20,590,381 high-quality single-nucleotide polymorphisms (SNP) and DNA insertions/deletions (InDels) were mined across 16 abaca cultivars. Filtering based on linkage disequilibrium (LD) yielded 130,768 SNPs and 13,620 InDels, accounting for 0.396 ± 0.106 and 0.431 ± 0.111 of gene diversity across these cultivars. LD-pruned polymorphisms across abaca, M. troglodytarum, M. acuminata and M. balbisiana enabled genetic differentiation within abaca and across the four Musa spp. Phylogenetic analysis revealed the registered varieties Abuab and Inosa to accumulate a significant number of mutations, eliciting further studies linking mutations to their advantageous phenotypes. Overall, this study pioneered in producing marker resources in abaca based on genome-wide polymorphisms vital for varietal authentication and comparative genotyping with the more studied Musa spp.
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Affiliation(s)
- Cris Francis C Barbosa
- Philippine Fiber Industry Development Authority (PhilFIDA), PCAF Building, Department of Agriculture (DA) Compound, Quezon City 1101, Philippines
- Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City 1101, Philippines
| | - Jayson C Asunto
- Philippine Fiber Industry Development Authority (PhilFIDA), PCAF Building, Department of Agriculture (DA) Compound, Quezon City 1101, Philippines
| | - Rhosener Bhea L Koh
- National Institute of Molecular Biology and Biotechnology, University of the Philippines Diliman, Quezon City 1101, Philippines
| | - Daisy May C Santos
- Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City 1101, Philippines
| | - Dapeng Zhang
- Sustainable Perennial Crops Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD 20705, USA
| | - Ernelea P Cao
- Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City 1101, Philippines
| | - Leny C Galvez
- Philippine Fiber Industry Development Authority (PhilFIDA), PCAF Building, Department of Agriculture (DA) Compound, Quezon City 1101, Philippines
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Liu Z, Zhao Y, Zhang Y, Xu L, Zhou L, Yang W, Zhao H, Zhao J, Wang F. Development of Omni InDel and supporting database for maize. FRONTIERS IN PLANT SCIENCE 2023; 14:1216505. [PMID: 37457340 PMCID: PMC10344896 DOI: 10.3389/fpls.2023.1216505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023]
Abstract
Insertions-deletions (InDels) are the second most abundant molecular marker in the genome and have been widely used in molecular biology research along with simple sequence repeats (SSR) and single-nucleotide polymorphisms (SNP). However, InDel variant mining and marker development usually focuses on a single type of dimorphic InDel, which does not reflect the overall InDel diversity across the genome. Here, we developed Omni InDels for maize, soybean, and rice based on sequencing data and genome assembly that included InDel variants with base lengths from 1 bp to several Mb, and we conducted a detailed classification of Omni InDels. Moreover, we screened a set of InDels that are easily detected and typed (Perfect InDels) from the Omni InDels, verified the site authenticity using 3,587 germplasm resources from 11 groups, and analyzed the germplasm resources. Furthermore, we developed a Multi-InDel set based on the Omni InDels; each Multi-InDel contains multiple InDels, which greatly increases site polymorphism, they can be detected in multiple platforms such as fluorescent capillary electrophoresis and sequencing. Finally, we developed an online database website to make Omni InDels easy to use and share and developed a visual browsing function called "Variant viewer" for all Omni InDel sites to better display the variant distribution.
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Affiliation(s)
- Zhihao Liu
- Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Beijing Academy of Agricultural and Forest Sciences (BAAFS), Beijing, China
- College of Agriculture, Jilin Agricultural University, Changchun, China
| | - Yikun Zhao
- Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Beijing Academy of Agricultural and Forest Sciences (BAAFS), Beijing, China
| | - Yunlong Zhang
- Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Beijing Academy of Agricultural and Forest Sciences (BAAFS), Beijing, China
| | - Liwen Xu
- Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Beijing Academy of Agricultural and Forest Sciences (BAAFS), Beijing, China
| | - Ling Zhou
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Weiguang Yang
- College of Agriculture, Jilin Agricultural University, Changchun, China
| | - Han Zhao
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Jiuran Zhao
- Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Beijing Academy of Agricultural and Forest Sciences (BAAFS), Beijing, China
| | - Fengge Wang
- Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Beijing Academy of Agricultural and Forest Sciences (BAAFS), Beijing, China
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Maan SS, Brar JS, Mittal A, Gill MIS, Arora NK, Sohi HS, Chhuneja P, Dhillon GS, Singh N, Thakur S. Construction of a genetic linkage map and QTL mapping of fruit quality traits in guava ( Psidium guajava L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1123274. [PMID: 37426984 PMCID: PMC10324979 DOI: 10.3389/fpls.2023.1123274] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/08/2023] [Indexed: 07/11/2023]
Abstract
Guava (Psidium guajava L.) is an important fruit crop of the Indian sub-continent, with potential for improvements in quality and yield. The goal of the present study was to construct a genetic linkage map in an intraspecific cross between the elite cultivar 'Allahabad Safeda' and the Purple Guava landrace to identify the genomic regions responsible for important fruit quality traits, viz., total soluble solids, titratable acidity, vitamin C, and sugars. This population was phenotyped in field trials (as a winter crop) for three consecutive years, and showed moderate-to-high values of heterogeneity coefficients along with higher heritability (60.0%-97.0%) and genetic-advance-over-mean values (13.23%-31.17%), suggesting minimal environmental influence on the expression of fruit-quality traits and indicating that these traits can be improved by phenotypic selection methods. Significant correlations and strong associations were also detected among fruit physico-chemical traits in segregating progeny. The constructed linkage map consisted of 195 markers distributed across 11 chromosomes, spanning a length of 1,604.47 cM (average inter-loci distance of 8.80 markers) and with 88.00% coverage of the guava genome. Fifty-eight quantitative trait loci (QTLs) were detected in three environments with best linear unbiased prediction (BLUP) values using the composite interval mapping algorithm of the BIP (biparental populations) module. The QTLs were distributed on seven different chromosomes, explaining 10.95%-17.77% of phenotypic variance, with the highest LOD score being 5.96 for qTSS.AS.pau-6.2. Thirteen QTLs detected across multiple environments with BLUPs indicate stability and utility in a future breeding program for guava. Furthermore, seven QTL clusters with stable or common individual QTLs affecting two or more different traits were located on six linkage groups (LGs), explaining the correlation among fruit-quality traits. Thus, the multiple environmental evaluations conducted here have increased our understanding of the molecular basis of phenotypic variation, providing the basis for future high-resolution fine-mapping and paving the way for marker-assisted breeding of fruit-quality traits.
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Affiliation(s)
| | | | - Amandeep Mittal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | | | - Naresh Kumar Arora
- Department of Fruit Science, Punjab Agricultural University, Ludhiana, India
| | - Harjot Singh Sohi
- Krishi Vigyan Kendra, Guru Angad Dev Veterinary and Animal Sciences University, Barnala, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | | | - Navdeep Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Sujata Thakur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
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Feng S, Wu J, Chen K, Chen M, Zhu Z, Wang J, Chen G, Cao B, Lei J, Chen C. Identification and characterization analysis of candidate genes controlling mushroom leaf development in Chinese kale by BSA-seq. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:17. [PMID: 37313295 PMCID: PMC10248679 DOI: 10.1007/s11032-023-01364-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/22/2023] [Indexed: 06/15/2023]
Abstract
Mushroom leaves (MLs) are malformed leaves that develop from the leaf veins in some of Chinese kale genotypes. To study the genetic model and molecular mechanism of ML development in Chinese kale, the F2 segregation population was constructed by two inbred lines, genotype Boc52 with ML and genotype Boc55 with normal leaves (NL). In the present study, we have identified for the first time that the development of mushroom leaves may be affected by the change of adaxial-abaxial polarity of leaves. Examination of the phenotypes of F1 and F2 segregation populations suggested that ML development is controlled by two dominant major genes inherited independently. BSA-seq analysis showed that a major quantitative trait locus (QTL) qML4.1 that controls ML development is located within 7.4 Mb on chromosome kC4. The candidate region was further narrowed to 255 kb by linkage analysis combined with insertion/deletion (InDel) markers, and 37 genes were predicted in this region. According to the expression and annotation analysis, a B3 domain-containing transcription factor NGA1-like gene, BocNGA1, was identified as a key candidate gene for controlling ML development in Chinese kale. Fifteen single nucleotide polymorphisms (SNPs) were found in coding sequences and 21 SNPs and 3 InDels found in the promoter sequences of BocNGA1 from the genotype Boc52 with ML. The expression levels of BocNGA1 in ML genotypes are significantly lower than in the NL genotypes, which suggests that BocNGA1 may act as a negative regulator for ML genesis in Chinese kale. This study provides a new foundation for Chinese kale breeding and for the study of the molecular mechanism of plant leaf differentiation. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01364-6.
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Affiliation(s)
- Shuo Feng
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Jianbing Wu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Kunhao Chen
- Guangdong Helinong Agricultural Research Institute Co., Ltd, Shantou, 515800 Guangdong China
- Guangdong Helinong Biological Seed Industry Co., Ltd, Shantou, 515800 Guangdong China
| | - Muxi Chen
- Guangdong Helinong Agricultural Research Institute Co., Ltd, Shantou, 515800 Guangdong China
- Guangdong Helinong Biological Seed Industry Co., Ltd, Shantou, 515800 Guangdong China
| | - Zhangsheng Zhu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Juntao Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Guoju Chen
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Bihao Cao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Jianjun Lei
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Changming Chen
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
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10
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Barmukh R, Roorkiwal M, Dixit GP, Bajaj P, Kholova J, Smith MR, Chitikineni A, Bharadwaj C, Sreeman SM, Rathore A, Tripathi S, Yasin M, Vijayakumar AG, Rao Sagurthi S, Siddique KHM, Varshney RK. Characterization of 'QTL-hotspot' introgression lines reveals physiological mechanisms and candidate genes associated with drought adaptation in chickpea. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7255-7272. [PMID: 36006832 PMCID: PMC9730794 DOI: 10.1093/jxb/erac348] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/24/2022] [Indexed: 05/16/2023]
Abstract
'QTL-hotspot' is a genomic region on linkage group 04 (CaLG04) in chickpea (Cicer arietinum) that harbours major-effect quantitative trait loci (QTLs) for multiple drought-adaptive traits, and it therefore represents a promising target for improving drought adaptation. To investigate the mechanisms underpinning the positive effects of 'QTL-hotspot' on seed yield under drought, we introgressed this region from the ICC 4958 genotype into five elite chickpea cultivars. The resulting introgression lines (ILs) and their parents were evaluated in multi-location field trials and semi-controlled conditions. The results showed that the 'QTL-hotspot' region improved seed yield under rainfed conditions by increasing seed weight, reducing the time to flowering, regulating traits related to canopy growth and early vigour, and enhancing transpiration efficiency. Whole-genome sequencing data analysis of the ILs and parents revealed four genes underlying the 'QTL-hotspot' region associated with drought adaptation. We validated diagnostic KASP markers closely linked to these genes using the ILs and their parents for future deployment in chickpea breeding programs. The CaTIFY4b-H2 haplotype of a potential candidate gene CaTIFY4b was identified as the superior haplotype for 100-seed weight. The candidate genes and superior haplotypes identified in this study have the potential to serve as direct targets for genetic manipulation and selection for chickpea improvement.
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Affiliation(s)
- Rutwik Barmukh
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | - Manish Roorkiwal
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia, Australia
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Girish P Dixit
- ICAR - Indian Institute of Pulses Research (IIPR), Kanpur, India
| | - Prasad Bajaj
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Jana Kholova
- Crops Physiology & Modeling, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Information Technologies, Faculty of Economics and Management, Czech University of Life Sciences Prague, Kamýcká 129, Prague, Czech Republic
| | - Millicent R Smith
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Australia
| | - Annapurna Chitikineni
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Chellapilla Bharadwaj
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia, Australia
- ICAR - Indian Agricultural Research Institute (IARI), Delhi, India
| | - Sheshshayee M Sreeman
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
| | - Abhishek Rathore
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Mohammad Yasin
- RAK College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior, India
| | | | | | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia, Australia
| | - Rajeev K Varshney
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia, Australia
- Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Murdoch, Western Australia, Australia
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11
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Liu K, Xie N. Pipeline for developing polymorphic microsatellites in species without reference genomes. 3 Biotech 2022; 12:248. [PMID: 36039078 PMCID: PMC9418399 DOI: 10.1007/s13205-022-03313-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/16/2022] [Indexed: 11/01/2022] Open
Abstract
Microsatellites, also known as simple sequence repeats (SSRs), are the preferred type of marker for many genetic applications. In conjunction with the ongoing development of next-generation sequencing, several bioinformatic tools have been developed for identifying SSRs from genomic or transcriptomic sequences. Although these tools are handy for generating polymorphic SSRs, their application almost always depends on an existing reference genome or self-assembly of the reference genome. With this in mind, we propose a pipeline for developing polymorphic SSRs that may be applied to species without reference genomes. Using a species without a reference genome (black Amur bream; Megalobrama terminalis Richardson, 1846) as a model, our pipeline was able to effectively discover polymorphic SSRs. Under different R parameters of a reference-free single nucleotide polymorphisms (SNPs) caller (ebwt2InDel), a total of 258, 208, 102, and 11 polymorphic SSRs were mined. To quantify the accuracy of the polymorphic SSRs detected using our pipeline, we analyzed 25 SSRs with PCR experiments. All primers were successfully amplified, and most SSRs (23 SSRs, 92%) were polymorphic. From the 36 individual black Amur bream, we acquired an average of 3.36 alleles per locus, ranging from one to 11. This demonstrates the effectiveness of our pipeline in identifying polymorphic SSRs and designing primers for SSR genotyping. Ultimately, our pipeline can effectively mine polymorphic SSRs for species without reference genomes, complementing SSR mining approaches based on reference genomes and helping to resolve biological issues that accompany these methods. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03313-0.
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Affiliation(s)
- Kai Liu
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, Zhejiang China
| | - Nan Xie
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, Zhejiang China
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12
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Du J, Li S, Shao J, Song H, Jiang P, Lei C, Bai J, Han L. Genetic diversity analysis and development of molecular markers for the identification of largemouth bass (Micropterus salmoides L.) based on whole-genome re-sequencing. Front Genet 2022; 13:936610. [PMID: 36105092 PMCID: PMC9465168 DOI: 10.3389/fgene.2022.936610] [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: 05/05/2022] [Accepted: 07/21/2022] [Indexed: 11/28/2022] Open
Abstract
Largemouth bass (Micropterus salmoides L.) is generally considered to comprise two subspecies, Florida bass (M. floridanus) and Northern Largemouth bass (M. salmoides), which have biological characteristic differences because of their geographical distribution. In this study, whole-genome re-sequencing was performed among 10 Florida and 10 Northern largemouth bass, respectively. In total, 999,793 SNPs and 227,797 InDels were finally identified, and 507,401 SNPs (50.75%) and 116,213 InDels (51.01%) were successfully mapped to annotated 18,629 genes and 14,060 genes, respectively. KEGG classification indicated that most of these genes were focused on the pathways including signal transduction, transport and catabolism, and endocrine system. Genetic diversity analysis indicated that Florida largemouth bass had higher genetic diversity than Northern largemouth bass, indicating that the germplasm quality of Northern largemouth bass had markedly reduced in China. To examine the accuracies of the identified markers, 23 SNPs and eight InDels (the insertions or deletions of more than 45 bp) were randomly selected and detected among Florida largemouth bass, Northern largemouth bass, and their F1 hybrids. The detection efficiencies of all the markers were higher than 95%; nineteen SNPs and three InDels could accurately distinguish the two subspecies and their F1 hybrids with 100% efficiencies. Moreover, the three InDel markers could clearly distinguish the two subspecies and their F1 hybrids with a PCR-based agarose gel electrophoresis. In conclusion, our study established a simple PCR-based method for the germplasm identification of largemouth bass, which will be useful in the germplasm protection, management, and hybridization breeding of largemouth bass.
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Affiliation(s)
- Jinxing Du
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Shengjie Li
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- *Correspondence: Shengjie Li,
| | - Jiaqi Shao
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Hongmei Song
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Peng Jiang
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Caixia Lei
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Junjie Bai
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Linqiang Han
- Guangdong Liangshi Aquatic Seed Industry Co Ltd, Foshan, China
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13
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Salgotra RK, Stewart CN. Genetic Augmentation of Legume Crops Using Genomic Resources and Genotyping Platforms for Nutritional Food Security. PLANTS (BASEL, SWITZERLAND) 2022; 11:1866. [PMID: 35890499 PMCID: PMC9325189 DOI: 10.3390/plants11141866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 11/24/2022]
Abstract
Recent advances in next generation sequencing (NGS) technologies have led the surge of genomic resources for the improvement legume crops. Advances in high throughput genotyping (HTG) and high throughput phenotyping (HTP) enable legume breeders to improve legume crops more precisely and efficiently. Now, the legume breeder can reshuffle the natural gene combinations of their choice to enhance the genetic potential of crops. These genomic resources are efficiently deployed through molecular breeding approaches for genetic augmentation of important legume crops, such as chickpea, cowpea, pigeonpea, groundnut, common bean, lentil, pea, as well as other underutilized legume crops. In the future, advances in NGS, HTG, and HTP technologies will help in the identification and assembly of superior haplotypes to tailor the legume crop varieties through haplotype-based breeding. This review article focuses on the recent development of genomic resource databases and their deployment in legume molecular breeding programmes to secure global food security.
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Affiliation(s)
- Romesh K. Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, Chatha, Jammu 190008, India
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14
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Bashir NH, Wang W, Ling X, Zhang J, Lu Q, He R, Chen H. Characterization of Potential Molecular Markers in Lac Insect Kerria lacca (Kerr) Responsible for Lac Production. INSECTS 2022; 13:545. [PMID: 35735882 PMCID: PMC9225327 DOI: 10.3390/insects13060545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 02/04/2023]
Abstract
Kerria lacca (Kerr) is an important lac insect extensively used in industrial products in the form of resin, wax and dye. The scarce knowledge on molecular markers for K. lacca is a barrier in elucidating genetic information. Our study identified a total of 16,921 single-nucleotide polymorphisms (SNPs), and 6231 insertions and deletions (InDels)-of which, intergenic variation accounted for 41.22% and 56.30%, and exonic variation accounted for 39.10% and 17.46%, of SNPs and InDels, respectively. Observation of SNPs suggested that nucleotide substitution frequency and transition to transversion (Ts/Tv) ratio were highest at the late adult stage, 3.97, compared to at the other stages, with a genome-wide Ts/Tv ratio of 2.95. The maximum number of SNPs, 2853 (16.86%), was identified in chromosome 8, while the lowest, 1126 (6.65%), was identified in chromosome 7. The maximum and minimum numbers of InDels were located on chromosome 1 and 7, with 834 (13.38%) and 519 (8.33%), respectively. Annotation showed that highest numbers of exonic and intergenic SNPs were present at the late adult stage, whereas the maximum number of InDels was found at the larval stage. On the basis of gene function, 47 gene variations were screened and 23 candidate genes were identified in associations with lac production. Concluding work will enhance knowledge on molecular markers to facilitate an increase in lac production in K. lacca as well as other lac insects.
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Affiliation(s)
- Nawaz Haider Bashir
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650224, China; (N.H.B.); (W.W.); (X.L.); (J.Z.); (Q.L.); (R.H.)
| | - Weiwei Wang
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650224, China; (N.H.B.); (W.W.); (X.L.); (J.Z.); (Q.L.); (R.H.)
| | - Xiaofei Ling
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650224, China; (N.H.B.); (W.W.); (X.L.); (J.Z.); (Q.L.); (R.H.)
| | - Jinwen Zhang
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650224, China; (N.H.B.); (W.W.); (X.L.); (J.Z.); (Q.L.); (R.H.)
| | - Qin Lu
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650224, China; (N.H.B.); (W.W.); (X.L.); (J.Z.); (Q.L.); (R.H.)
| | - Rui He
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650224, China; (N.H.B.); (W.W.); (X.L.); (J.Z.); (Q.L.); (R.H.)
| | - Hang Chen
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650224, China; (N.H.B.); (W.W.); (X.L.); (J.Z.); (Q.L.); (R.H.)
- The Key Laboratory of Cultivating and Utilization of Resources Insects, State Forestry Administration, Kunming 650224, China
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15
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Zhang H, Tang S, Schnable JC, He Q, Gao Y, Luo M, Jia G, Feng B, Zhi H, Diao X. Genome-Wide DNA Polymorphism Analysis and Molecular Marker Development for the Setaria italica Variety "SSR41" and Positional Cloning of the Setaria White Leaf Sheath Gene SiWLS1. FRONTIERS IN PLANT SCIENCE 2021; 12:743782. [PMID: 34858451 PMCID: PMC8632227 DOI: 10.3389/fpls.2021.743782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/13/2021] [Indexed: 05/03/2023]
Abstract
Genome-wide DNA polymorphism analysis and molecular marker development are important for forward genetics research and DNA marker-assisted breeding. As an ideal model system for Panicoideae grasses and an important minor crop in East Asia, foxtail millet (Setaria italica) has a high-quality reference genome as well as large mutant libraries based on the "Yugu1" variety. However, there is still a lack of genetic and mutation mapping tools available for forward genetics research on S. italica. Here, we screened another S. italica genotype, "SSR41", which is morphologically similar to, and readily cross-pollinates with, "Yugu1". High-throughput resequencing of "SSR41" identified 1,102,064 reliable single nucleotide polymorphisms (SNPs) and 196,782 insertions/deletions (InDels) between the two genotypes, indicating that these two genotypes have high genetic diversity. Of the 8,361 high-quality InDels longer than 20 bp that were developed as molecular markers, 180 were validated with 91.5% accuracy. We used "SSR41" and these developed molecular markers to map the white leaf sheath gene SiWLS1. Further analyses showed that SiWLS1 encodes a chloroplast-localized protein that is involved in the regulation of chloroplast development in bundle sheath cells in the leaf sheath in S. italica and is related to sensitivity to heavy metals. Our study provides the methodology and an important resource for forward genetics research on Setaria.
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Affiliation(s)
- Hui Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Sha Tang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - James C. Schnable
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE, United States
| | - Qiang He
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuanzhu Gao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mingzhao Luo
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guanqing Jia
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Baili Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Hui Zhi
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xianmin Diao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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16
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Thakur S, Yadav IS, Jindal M, Sharma PK, Dhillon GS, Boora RS, Arora NK, Gill MIS, Chhuneja P, Mittal A. Development of Genome-Wide Functional Markers Using Draft Genome Assembly of Guava ( Psidium guajava L.) cv. Allahabad Safeda to Expedite Molecular Breeding. FRONTIERS IN PLANT SCIENCE 2021; 12:708332. [PMID: 34630458 PMCID: PMC8494772 DOI: 10.3389/fpls.2021.708332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Guava (Psidium guajava L.), a rich source of nutrients, is an important tropical and subtropical fruit of the Myrtaceae family and exhibits magnificent diversity. Genetic diversity analysis is the first step toward the identification of parents for hybridization, genetic mapping, and molecular breeding in any crop species. A diversity analysis based on whole-genome functional markers increases the chances of identifying genetic associations with agronomically important traits. Therefore, here, we sequenced the genome of guava cv. Allahabad Safeda on an Illumina platform and generated a draft assembly of ~304 MB. The assembly of the Allahabad Safeda genome constituted >37.95% repeat sequences, gene prediction with RNA-seq data as evidence identified 14,115 genes, and BLAST n/r, Interproscan, PfamScan, BLAST2GO, and KEGG annotated 13,957 genes. A comparative protein transcript analysis of tree species revealed the close relatedness of guava with Eucalyptus. Comparative transcriptomics-based SSR/InDel/SNP-PCR ready genome-wide markers in greenish-yellow skinned and white fleshed-Allahabad Safeda to four contrasting cultivars viz apple-color-skinned and white-fleshed-Lalima, greenish-yellow-skinned and pink-fleshed-Punjab Pink, purple-black-skinned and purple-fleshed-Purple Local and widely used rootstock-Lucknow-49 were developed. The molecular markers developed here revealed a high level of individual heterozygosity within genotypes in 22 phenotypically diverse guava cultivars. Principal coordinate, STRUCTURE clustering, and neighbor-joining-based genetic diversity analysis identified distinct clusters associated with fruit skin and flesh color. The genome sequencing of guava, functional annotation, comparative transcriptomics-based genome-wide markers, and genetic diversity analysis will expand the knowledge of genomes of climacteric fruits, facilitating trait-based molecular breeding and diversifying the nutritional basket.
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Affiliation(s)
- Sujata Thakur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Inderjit Singh Yadav
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Manish Jindal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Parva Kumar Sharma
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | | | - Rajbir Singh Boora
- Fruit Research Sub-Station, Punjab Agricultural University, Bahadurgarh, India
| | - Naresh Kumar Arora
- Department of Fruit Science, Punjab Agricultural University, Ludhiana, India
| | | | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Amandeep Mittal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
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17
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Pan G, Li Z, Huang S, Tao J, Shi Y, Chen A, Li J, Tang H, Chang L, Deng Y, Li D, Zhao L. Genome-wide development of insertion-deletion (InDel) markers for Cannabis and its uses in genetic structure analysis of Chinese germplasm and sex-linked marker identification. BMC Genomics 2021; 22:595. [PMID: 34353285 PMCID: PMC8340516 DOI: 10.1186/s12864-021-07883-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/28/2021] [Indexed: 12/30/2022] Open
Abstract
Background Cannabis sativa L., a dioecious plant derived from China, demonstrates important medicinal properties and economic value worldwide. Cannabis properties have been usually harnessed depending on the sex of the plant. To analyse the genetic structure of Chinese Cannabis and identify sex-linked makers, genome-wide insertion-deletion (InDel) markers were designed and used. Results In this study, a genome-wide analysis of insertion-deletion (InDel) polymorphisms was performed based on the recent genome sequences. In total, 47,558 InDels were detected between the two varieties, and the length of InDels ranged from 4 bp to 87 bp. The most common InDels were tetranucleotides, followed by pentanucleotides. Chromosome 5 exhibited the highest number of InDels among the Cannabis chromosomes, while chromosome 10 exhibited the lowest number. Additionally, 31,802 non-redundant InDel markers were designed, and 84 primers evenly distributed in the Cannabis genome were chosen for polymorphism analysis. A total of 38 primers exhibited polymorphisms among three accessions, and of the polymorphism primers, 14 biallelic primers were further used to analyse the genetic structure. A total of 39 fragments were detected, and the PIC value ranged from 0.1209 to 0.6351. According to the InDel markers and the flowering time, the 115 Chinese germplasms were divided into two subgroups, mainly composed of cultivars obtained from the northernmost and southernmost regions, respectively. Additional two markers, “Cs-I1–10” and “Cs-I1–15”, were found to amplify two bands (398 bp and 251 bp; 293 bp and 141 bp) in the male plants, while 389-bp or 293-bp bands were amplified in female plants. Using the two markers, the feminized and dioecious varieties could also be distinguished. Conclusion Based on the findings obtained herein, we believe that this study will facilitate the genetic improvement and germplasm conservation of Cannabis in China, and the sex-linked InDel markers will provide accurate sex identification strategies for Cannabis breeding and production. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07883-w.
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Affiliation(s)
- Gen Pan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.,Key Laboratory of the Biology and Process of Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Zheng Li
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Siqi Huang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.,Key Laboratory of the Biology and Process of Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Jie Tao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Yaliang Shi
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Anguo Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.,Key Laboratory of the Biology and Process of Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Jianjun Li
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.,Key Laboratory of the Biology and Process of Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Huijuan Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.,Key Laboratory of the Biology and Process of Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Li Chang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.,Key Laboratory of the Biology and Process of Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Yong Deng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.,Key Laboratory of the Biology and Process of Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Defang Li
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China. .,Key Laboratory of the Biology and Process of Bast Fiber Crops, Ministry of Agriculture, Changsha, China.
| | - Lining Zhao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China. .,Key Laboratory of the Biology and Process of Bast Fiber Crops, Ministry of Agriculture, Changsha, China.
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18
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Barmukh R, Soren KR, Madugula P, Gangwar P, Shanmugavadivel PS, Bharadwaj C, Konda AK, Chaturvedi SK, Bhandari A, Rajain K, Singh NP, Roorkiwal M, Varshney RK. Construction of a high-density genetic map and QTL analysis for yield, yield components and agronomic traits in chickpea (Cicer arietinum L.). PLoS One 2021; 16:e0251669. [PMID: 33989359 PMCID: PMC8121343 DOI: 10.1371/journal.pone.0251669] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/30/2021] [Indexed: 12/04/2022] Open
Abstract
Unravelling the genetic architecture underlying yield components and agronomic traits is important for enhancing crop productivity. Here, a recombinant inbred line (RIL) population, developed from ICC 4958 and DCP 92–3 cross, was used for constructing linkage map and QTL mapping analysis. The RIL population was genotyped using a high-throughput Axiom®CicerSNP array, which enabled the development of a high-density genetic map consisting of 3,818 SNP markers and spanning a distance of 1064.14 cM. Analysis of phenotyping data for yield, yield components and agronomic traits measured across three years together with genetic mapping data led to the identification of 10 major-effect QTLs and six minor-effect QTLs explaining up to 59.70% phenotypic variance. The major-effect QTLs identified for 100-seed weight, and plant height possessed key genes, such as C3HC4 RING finger protein, pentatricopeptide repeat (PPR) protein, sugar transporter, leucine zipper protein and NADH dehydrogenase, amongst others. The gene ontology studies highlighted the role of these genes in regulating seed weight and plant height in crop plants. The identified genomic regions for yield, yield components, and agronomic traits, and the closely linked markers will help advance genetics research and breeding programs in chickpea.
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Affiliation(s)
- Rutwik Barmukh
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | | | - Praveen Madugula
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | | | | | | | - Sushil K. Chaturvedi
- ICAR-Indian Institute of Pulses Research, Kanpur, UP, India
- Rani Lakshmi Bai Central Agricultural University, Jhansi, India
| | - Aditi Bhandari
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Kritika Rajain
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Narendra Pratap Singh
- ICAR-Indian Institute of Pulses Research, Kanpur, UP, India
- * E-mail: (RKV); (MR); (NPS)
| | - Manish Roorkiwal
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- * E-mail: (RKV); (MR); (NPS)
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- * E-mail: (RKV); (MR); (NPS)
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Barmukh R, Roorkiwal M, Jaba J, Chitikineni A, Mishra SP, Sagurthi SR, Munghate R, Sharma HC, Varshney RK. Development of a dense genetic map and QTL analysis for pod borer Helicoverpa armigera (Hübner) resistance component traits in chickpea (Cicer arietinum L.). THE PLANT GENOME 2020; 14:e20071. [PMID: 33289349 DOI: 10.1002/tpg2.20071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/15/2020] [Indexed: 06/12/2023]
Abstract
Genetic enhancement for resistance against the pod borer, Helicoverpa armigera is crucial for enhancing production and productivity of chickpea. Here we provide some novel insights into the genetic architecture of natural variation in H. armigera resistance in chickpea, an important legume, which plays a major role in food and nutritional security. An interspecific recombinant inbred line (RIL) population developed from a cross between H. armigera susceptible accession ICC 4958 (Cicer arietinum) and resistant accession PI 489777 (Cicer reticulatum) was evaluated for H. armigera resistance component traits using detached leaf assay and under field conditions. A high-throughput AxiomCicerSNP array was utilized to construct a dense linkage map comprising of 3,873 loci and spanning a distance of 949.27 cM. Comprehensive analyses of extensive genotyping and phenotyping data identified nine main-effect QTLs and 955 epistatic QTLs explaining up to 42.49% and 38.05% phenotypic variance, respectively, for H. armigera resistance component traits. The main-effect QTLs identified in this RIL population were linked with previously described genes, known to modulate resistance against lepidopteran insects in crop plants. One QTL cluster harbouring main-effect QTLs for three H. armigera resistance component traits and explaining up to 42.49% of the phenotypic variance, was identified on CaLG03. This genomic region, after validation, may be useful to improve H. armigera resistance component traits in elite chickpea cultivars.
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Affiliation(s)
- Rutwik Barmukh
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | - Manish Roorkiwal
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Jagdish Jaba
- Theme-Integrated Crop Management, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Suraj Prasad Mishra
- Theme-Integrated Crop Management, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Rajendra Munghate
- Theme-Integrated Crop Management, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - H C Sharma
- Theme-Integrated Crop Management, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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Wang X, Shen F, Gao Y, Wang K, Chen R, Luo J, Yang L, Zhang X, Qiu C, Li W, Wu T, Xu X, Wang Y, Cong P, Han Z, Zhang X. Application of genome-wide insertion/deletion markers on genetic structure analysis and identity signature of Malus accessions. BMC PLANT BIOLOGY 2020; 20:540. [PMID: 33256591 PMCID: PMC7708918 DOI: 10.1186/s12870-020-02744-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 11/17/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Apple (Malus ssp.), one of the most important temperate fruit crops, has a long cultivation history and is economically important. To identify the genetic relationships among the apple germplasm accessions, whole-genome structural variants identified between M. domestica cultivars 'Jonathan' and 'Golden Delicious' were used. RESULTS A total of 25,924 insertions and deletions (InDels) were obtained, from which 102 InDel markers were developed. Using the InDel markers, we found that 942 (75.3%) of the 1251 Malus accessions from 35 species exhibited a unique identity signature due to their distinct genotype combinations. The 102 InDel markers could distinguish 16.7-71.4% of the 331 bud sports derived from 'Fuji', 'Red Delicious', 'Gala', 'Golden Delicious', and other cultivars. Five distinct genetic patterns were found in 1002 diploid accessions based on 78 bi-allele InDel markers. Genetic structure analysis indicated that M. domestica showed higher genetic diversity than the other species. Malus underwent a relatively high level of wild-to-crop or crop-to-wild gene flow. M. sieversii was closely related to both M. domestica and cultivated Chinese cultivars. CONCLUSIONS The identity signatures of Malus accessions can be used to determine distinctness, uniformity, and stability. The results of this study may also provide better insight into the genetic relationships among Malus species.
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Affiliation(s)
- Xuan Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Fei Shen
- College of Horticulture, China Agricultural University, Beijing, China
- Beijing Agro-biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yuan Gao
- Research Institute of Pomology, Chinese Academy of Agricultural Science, Xingcheng, Liaoning, China
| | - Kun Wang
- Research Institute of Pomology, Chinese Academy of Agricultural Science, Xingcheng, Liaoning, China
| | - Ruiting Chen
- College of Horticulture, China Agricultural University, Beijing, China
- Present Address: Shaanxi Haisheng Fruit Industry Development Co., Ltd., Shaanxi, Xian, China
| | - Jun Luo
- College of Information and Electrical Engineering, China Agricultural University, Beijing, China
| | - Lili Yang
- College of Information and Electrical Engineering, China Agricultural University, Beijing, China
| | - Xi Zhang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Changpeng Qiu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Wei Li
- College of Horticulture, China Agricultural University, Beijing, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Peihua Cong
- Research Institute of Pomology, Chinese Academy of Agricultural Science, Xingcheng, Liaoning, China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing, China.
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Genome-Wide Discovery of InDel Markers in Sesame ( Sesamum indicum L.) Using ddRADSeq. PLANTS 2020; 9:plants9101262. [PMID: 32987937 PMCID: PMC7599716 DOI: 10.3390/plants9101262] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 01/15/2023]
Abstract
The development and validation of different types of molecular markers is crucial to conducting marker-assisted sesame breeding. Insertion-deletion (InDel) markers are highly polymorphic and suitable for low-cost gel-based genotyping. From this perspective, this study aimed to discover and develop InDel markers through bioinformatic analysis of double digest restriction site-associated DNA sequencing (ddRADSeq) data from 95 accessions belonging to the Mediterranean sesame core collection. Bioinformatic analysis indicated the presence of 7477 InDel positions genome wide. Deletions accounted for 61% of the InDels and short deletions (1-2 bp) were the most abundant type (94.9%). On average, InDels of at least 2 bp in length had a frequency of 2.99 InDels/Mb. The 86 InDel sites having length ≥8 bp were detected in genome-wide analysis. These regions can be used for the development of InDel markers considering low-cost genotyping with agarose gels. In order to validate these InDels, a total of 38 InDel regions were selected and primers were successfully amplified. About 13% of these InDels were in the coding sequences (CDSs) and in the 3'- and 5'- untranslated regions (UTRs). Furthermore, the efficiencies of these 16 InDel markers were assessed on 32 sesame accessions. The polymorphic information content (PIC) of these 16 markers ranged from 0.06 to 0.62 (average: 0.33). These results demonstrated the success of InDel identification and marker development for sesame with the use of ddRADSeq data. These agarose-resolvable InDel markers are expected to be useful for sesame breeders.
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Gene Pyramiding for Sustainable Crop Improvement against Biotic and Abiotic Stresses. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10091255] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Sustainable agricultural production is endangered by several ecological factors, such as drought, extreme temperatures, excessive salts, parasitic ailments, and insect pest infestation. These challenging environmental factors may have adverse effects on future agriculture production in many countries. In modern agriculture, conventional crop-breeding techniques alone are inadequate for achieving the increasing population’s food demand on a sustainable basis. The advancement of molecular genetics and related technologies are promising tools for the selection of new crop species. Gene pyramiding through marker-assisted selection (MAS) and other techniques have accelerated the development of durable resistant/tolerant lines with high accuracy in the shortest period of time for agricultural sustainability. Gene stacking has not been fully utilized for biotic stress resistance development and quality improvement in most of the major cultivated crops. This review emphasizes on gene pyramiding techniques that are being successfully deployed in modern agriculture for improving crop tolerance to biotic and abiotic stresses for sustainable crop improvement.
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Liang S, Lin F, Qian Y, Zhang T, Wu Y, Qi Y, Ren S, Ruan L, Zhao H. A cost-effective barcode system for maize genetic discrimination based on bi-allelic InDel markers. PLANT METHODS 2020; 16:101. [PMID: 32742299 PMCID: PMC7391534 DOI: 10.1186/s13007-020-00644-y] [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: 01/04/2020] [Accepted: 07/22/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Maize is one of the most important cereal crop all over the world with a complex genome of about 2.3 gigabase, and exhibits tremendous phenotypic and molecular diversity among different germplasms. Along with the phenotype identification, molecular markers have been accepted extensively as an alternative tool to discriminate different genotypes. RESULTS By using previous re-sequencing data of 205 lines, bi-allelic insertions and deletions (InDels) all over maize genome were screened, and a barcode system was constructed consisting of 37 bi-allelic insertion-deletion markers with high polymorphism information content (PIC) values, large discriminative size among varieties. The barcode system was measured and determined, different maize hybrids and inbreds were clearly discriminated efficiently with these markers, and hybrids responding parents were accurately determined. Compared with microarray data of more than 200 maize lines, the barcode system can discriminate maize varieties with 1.57% of different loci as a threshold. The barcode system can be used in standardized easy and quick operation with very low cost and minimum equipment requirements. CONCLUSION A barcode system was constructed for genetic discrimination of maize lines, including 37 InDel markers with high PIC values and user-friendly. The barcode system was measured and determined for efficient identification of maize lines.
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Affiliation(s)
- Shuaiqiang Liang
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Feng Lin
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yiliang Qian
- Anhui Academy of Agricultural Sciences, Hefei, China
| | - Tifu Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yibo Wu
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yaocheng Qi
- Anhui Academy of Agricultural Sciences, Hefei, China
| | - Sihai Ren
- Anhui Academy of Agricultural Sciences, Hefei, China
| | - Long Ruan
- Anhui Academy of Agricultural Sciences, Hefei, China
| | - Han Zhao
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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Genetic Dissection and Identification of Candidate Genes for Salinity Tolerance Using Axiom ®CicerSNP Array in Chickpea. Int J Mol Sci 2020; 21:ijms21145058. [PMID: 32709160 PMCID: PMC7404205 DOI: 10.3390/ijms21145058] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/10/2020] [Accepted: 07/14/2020] [Indexed: 01/22/2023] Open
Abstract
Globally, chickpea production is severely affected by salinity stress. Understanding the genetic basis for salinity tolerance is important to develop salinity tolerant chickpeas. A recombinant inbred line (RIL) population developed using parental lines ICCV 10 (salt-tolerant) and DCP 92-3 (salt-sensitive) was screened under field conditions to collect information on agronomy, yield components, and stress tolerance indices. Genotyping data generated using Axiom®CicerSNP array was used to construct a linkage map comprising 1856 SNP markers spanning a distance of 1106.3 cM across eight chickpea chromosomes. Extensive analysis of the phenotyping and genotyping data identified 28 quantitative trait loci (QTLs) explaining up to 28.40% of the phenotypic variance in the population. We identified QTL clusters on CaLG03 and CaLG06, each harboring major QTLs for yield and yield component traits under salinity stress. The main-effect QTLs identified in these two clusters were associated with key genes such as calcium-dependent protein kinases, histidine kinases, cation proton antiporter, and WRKY and MYB transcription factors, which are known to impart salinity stress tolerance in crop plants. Molecular markers/genes associated with these major QTLs, after validation, will be useful to undertake marker-assisted breeding for developing better varieties with salinity tolerance.
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Fan J, Xia Y, Wang GL. An improved heteroduplex analysis for rapid genotyping of SNPs and single base pair indels. Biotechniques 2019; 67:6-10. [PMID: 31124706 DOI: 10.2144/btn-2019-0012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
SNPs and single base pair (SBP) insertion/deletions (indels) are not only the most abundant genetic markers for genetic mapping and breeding selection, but also always occur in the mutants generated from chemical mutagenesis or CRISPR/Cas9-mediated genome editing. Most of the current SNP and SBP indel genotyping methods are time-consuming and/or require special equipment or reagents. Here, we describe an improved heteroduplex analysis method, named iHDA, that can readily discriminate SNP and SBP indel alleles with specially designed DNA probes that harbor a couple of nucleotides adjacent to the SNP site. By hybridizing with the same probe, SNP and SBP indel alleles form different heteroduplexes, differing in bulge size, which show different mobility on a polyacrylamide gel. Therefore, iHDA is an easy, fast and inexpensive method for SNP and SBP indel genotyping.
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Affiliation(s)
- Jiangbo Fan
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA.,State Key Laboratory for Biology of Plant Diseases & Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ye Xia
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA
| | - Guo-Liang Wang
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA.,State Key Laboratory for Biology of Plant Diseases & Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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