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Qiao L, Liu S, Li J, Li S, Yu Z, Liu C, Li X, Liu J, Ren Y, Zhang P, Zhang X, Yang Z, Chang Z. Development of Sequence-Tagged Site Marker Set for Identification of J, J S, and St Sub-genomes of Thinopyrum intermedium in Wheat Background. Front Plant Sci 2021; 12:685216. [PMID: 34249056 PMCID: PMC8261300 DOI: 10.3389/fpls.2021.685216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/14/2021] [Indexed: 06/13/2023]
Abstract
Thinopyrum intermedium (2n = 6x = 42, JJJSJSStSt) is one of the important resources for the wheat improvement. So far, a few Th. intermedium (Thi)-specific molecular markers have been reported, but the number is far from enough to meet the need of identifying alien fragments in wheat-Th. intermedium hybrids. In this study, 5,877,409 contigs were assembled using the Th. intermedium genotyping-by-sequencing (GBS) data. We obtained 5,452 non-redundant contigs containing mapped Thi-GBS markers with less than 20% similarity to the wheat genome and developed 2,019 sequence-tagged site (STS) molecular markers. Among the markers designed, 745 Thi-specific markers with amplification products in Th. intermedium but not in eight wheat landraces were further selected. The distribution of these markers in different homologous groups of Th. intermedium varied from 47 (7/12/28 on 6J/6St/6JS) to 183 (54/62/67 on 7J/7St/7JS). Furthermore, the effectiveness of these Thi-specific markers was verified using wheat-Th. intermedium partial amphidiploids, addition lines, substitution lines, and translocation lines. Markers developed in this study provide a convenient, rapid, reliable, and economical method for identifying Th. intermedium chromosomes in wheat. In addition, this set of Thi-specific markers can also be used to estimate genetic and physical locations of Th. intermedium chromatin in the introgression lines, thus providing valuable information for follow-up studies such as alien gene mining.
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Affiliation(s)
- Linyi Qiao
- College of Agriculture, Shanxi Agricultural University, Taiyuan, China
| | - Shujuan Liu
- Department of Plant Science, College of Agronomy, Northwest Agriculture & Forestry University, Yangling, China
| | - Jianbo Li
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
- School of Life and Environmental Sciences, Plant Breeding Institute, The University of Sydney, Cobbitty, NSW, Australia
| | - Shijiao Li
- Department of Botany, College of Life Science, Shanxi University, Taiyuan, China
| | - Zhihui Yu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Cheng Liu
- School of Life and Environmental Sciences, Plant Breeding Institute, The University of Sydney, Sydney, NSW, Australia
| | - Xin Li
- College of Agriculture, Shanxi Agricultural University, Taiyuan, China
| | - Jing Liu
- Department of Botany, College of Life Science, Shanxi University, Taiyuan, China
| | - Yongkang Ren
- College of Agriculture, Shanxi Agricultural University, Taiyuan, China
| | - Peng Zhang
- School of Life and Environmental Sciences, Plant Breeding Institute, The University of Sydney, Cobbitty, NSW, Australia
| | - Xiaojun Zhang
- College of Agriculture, Shanxi Agricultural University, Taiyuan, China
| | - Zujun Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhijian Chang
- College of Agriculture, Shanxi Agricultural University, Taiyuan, China
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Baksh SKY, Donde R, Kumar J, Mukherjee M, Meher J, Behera L, Dash SK. Genetic relationship, population structure analysis and pheno-molecular characterization of rice ( Oryza sativa L.) cultivars for bacterial leaf blight resistance and submergence tolerance using trait specific STS markers. Physiol Mol Biol Plants 2021; 27:543-562. [PMID: 33854283 PMCID: PMC7981353 DOI: 10.1007/s12298-021-00951-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/02/2021] [Accepted: 02/10/2021] [Indexed: 06/12/2023]
Abstract
UNLABELLED Rice is an important source of calorie for the growing world population. Its productivity, however is affected by climatic adversities, pest attacks, diseases of bacterial, viral and fungal origin and many other threats. Developing cultivars that are high yielding and stress resilient seems a better solution to tackle global food security issues. This study investigates the potential resistance of 24 rice cultivars against Xanthomonas oryzae pv. Oryzae (Xoo) infection that causes bacterial leaf blight disease and submergence stress. Bacterial leaf blight (BLB) resistance genes (Xa4, xa5, xa13, Xa21, Xa38) and submergence tolerance (Sub1) gene specific markers were used to determine the allelic status of genotypes. The results displayed presence of Xa4 resistance allele (78.95%), xa5 (15.79%) but xa13 and Sub1 tolerance allele were not found in any genotype. However, a new allele for Xa21 (84.21%) and Xa38 (10.52%) were identified in several genotypes. Phenotypic screening for both stress conditions was done to record the cultivars response. None of the genotypes showed resistance against Xoo, although varieties viz., Tapaswini and Konark showed moderate susceptibility. Likewise, survival percentage of genotypes under submergence stress varied from 0 to 100%. Tolerant checks FR13A (100%) and Swarna Sub1 (97.78%) exhibited high survival rate, whereas among genotypes, Gayatri (57.78%) recorded high survivability even though it lacked Sub1 tolerant its genetic background. A total of six trait specific STS and two SSR markers generated an average of 2.38 allele per locus. Polymorphism information content (PIC) value ranged from 0.08 to 0.42 with an average of 0.20. Structure analysis categorized 24 genotypes into two sub-populations, which was in correspondence with Nei's genetic distance-based NJ tree and principal co-ordinate analysis (PCoA). Swarna Sub1 could be differentiated clearly from BLB resistant check, IRBB60 and other 22 genotypes without having Sub1 gene. Analysis of molecular variance (AMOVA) revealed more genetic variation within population than among population. Principal component analysis (PCA) showed that 9 morphological traits collectively explained 76.126% of total variation among all the genotypes studied. The information from this study would be useful in future breeding programs for pyramiding trait specific genes into high yielding cultivars that fall behind with respect to stress resilience. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-00951-1.
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Affiliation(s)
- S. K. Yasin Baksh
- Crop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha 753006 India
| | - Ravindra Donde
- Crop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha 753006 India
| | - Jitendra Kumar
- Crop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha 753006 India
| | - Mitadru Mukherjee
- Crop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha 753006 India
| | - Jitendriya Meher
- Crop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha 753006 India
| | - Lambodar Behera
- Crop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha 753006 India
| | - Sushanta Kumar Dash
- Crop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha 753006 India
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Trojak-Goluch A, Skomra U. Ploidy variation and agronomic performance of F 1 hybrids of tetraploid and diploid forms of Humulus lupulus L. Breed Sci 2020; 70:176-182. [PMID: 32523399 PMCID: PMC7272252 DOI: 10.1270/jsbbs.19102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/01/2019] [Indexed: 06/11/2023]
Abstract
Humulus lupulus (2n = 2x = 20) as a source of hop resins, essential oils and polyphenols has value in brewing, pharmacy and cosmetology. Conventional crossing between tetraploids of 'Sybilla' and diploid males were performed to obtain F1 hybrids. Cytological studies revealed that 83.8% of the hybrids were triploids (2n = 3x = 30), 15.2% were aneuploids in which the chromosome number ranged from 28-32. Tetraploids (2n = 4x = 40) and diploids were also observed, which indicates numerous disturbances of gametogenesis of the parental forms. STS markers specific for male plants showed that females outnumbered male individuals among the F1 hybrids, which is in accordance with the distribution of sex ratio characteristic for diploid hybrids of H. lupulus. Female triploids were compared to the control 'Sybilla' with regard to their functional characteristics and alpha acids content in cones. A two year-long experiment showed that most of the triploids had a significantly higher position of fructiferous branches and shoot twist index compared to diploids of 'Sybilla'. There was also a significantly extended time for them to reach technological maturity of cones. Triploids were distinguished by a significantly lower seed content compared to 'Sybilla', therefore the raw material obtained from them is more suitable for the production of hop pellets and extracts.
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Affiliation(s)
- Anna Trojak-Goluch
- Department of Plant Breeding and Biotechnology, Institute of Soil Science and Plant Cultivation, State Research Institute, ul. Czartoryskich 8, PL-24-100 Pulawy, Poland
| | - Urszula Skomra
- Department of Plant Breeding and Biotechnology, Institute of Soil Science and Plant Cultivation, State Research Institute, ul. Czartoryskich 8, PL-24-100 Pulawy, Poland
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Hu CY, Tsai YZ, Lin SF. Development of STS and CAPS markers for variety identification and genetic diversity analysis of tea germplasm in Taiwan. Bot Stud 2014; 55:12. [PMID: 28510923 PMCID: PMC5430312 DOI: 10.1186/1999-3110-55-12] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 11/22/2013] [Indexed: 05/19/2023]
Abstract
BACKGROUND Tea (Camellia sinensis) is an important economic crop in Taiwan. Particularly, two major commercial types of tea (Paochong tea and Oolong tea) which are produced in Taiwan are famous around the world, and they must be manufactured with specific cultivars. Nevertheless, many elite cultivars have been illegally introduced to foreign countries. Because of the lower cost, large amount of "Taiwan-type tea" are produced and imported to Taiwan, causing a dramatic damage in the tea industry. It is very urgent to develop the stable, fast and reliable DNA markers for fingerprinting tea cultivars in Taiwan and protecting intellectual property rights for breeders. Furthermore, genetic diversity and phylogenetic relationship evaluations of tea germplasm in Taiwan are imperative for parental selection in the cross-breeding program and avoidance of genetic vulnerability. RESULTS Two STS and 37 CAPS markers derived from cytoplasmic genome and ESTs of tea have been developed in this study providing a useful tool for distinguishing all investigated germplasm. For identifying 12 prevailing tea cultivars in Taiwan, five core markers, including each one of mitochondria and chloroplast, and three nuclear markers, were developed. Based on principal coordinate analysis and cluster analysis, 55 tea germplasm in Taiwan were divided into three groups: sinensis type (C. sinensis var. sinensis), assamica type (C. sinensis var. assamica) and Taiwan wild species (C. formosensis). The result of genetic diversity analysis revealed that both sinensis (0.44) and assamica (0.41) types had higher genetic diversity than wild species (0.25). The close genetic distance between the first (Chin-Shin-Oolong) and the third (Shy-Jih-Chuen) prevailing cultivars was found, and many recently released varieties are the descents of Chin-Shin-Oolong. This implies the potential risk of genetic vulnerability for tea cultivation in Taiwan. CONCLUSIONS We have successfully developed a tool for tea germplasm discrimination and genetic diversity analysis, as well as a set of core markers for effective identification of prevailing cultivars in Taiwan. According to the results of phylogenetic analysis on prevailing tea cultivars, it is necessary to broaden genetic diversity from wild species or plant introduction in future breeding programs.
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Affiliation(s)
- Chih-Yi Hu
- Department of Agronomy, National Taiwan University, Taipei, 106 Taiwan
- Wunshan Branch, Tea Research and Extension Station, Council of Agriculture, Executive Yuan, New Taipei City, 231 Taiwan
| | - You-Zen Tsai
- Tea Research and Extension Station, Council of Agriculture, Executive Yuan, Taoyuan, 324 Taiwan
| | - Shun-Fu Lin
- Department of Agronomy, National Taiwan University, Taipei, 106 Taiwan
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