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Türkösi E, Szakács É, Ivanizs L, Farkas A, Gaál E, Said M, Darkó É, Cséplő M, Mikó P, Doležel J, Molnár-Láng M, Molnár I, Kruppa K. A chromosome arm from Thinopyrum intermedium × Thinopyrum ponticum hybrid confers increased tillering and yield potential in wheat. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:7. [PMID: 38263978 PMCID: PMC10803699 DOI: 10.1007/s11032-024-01439-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 12/25/2023] [Indexed: 01/25/2024]
Abstract
Tiller number is a key component of wheat plant architecture having a direct impact on grain yield. Because of their viability, biotic resistance, and abiotic stress tolerance, wild relative species are a valuable gene source for increasing wheat genetic diversity, including yield potential. Agropyron glael, a perennial hybrid of Thinopyrum intermedium and Th. ponticum, was created in the 1930s. Recent genome analyses identified five evolutionarily distinct subgenomes (J, Jst, Jvs, Jr, and St), making A. glael an important gene source for transferring useful agronomical traits into wheat. During a bread wheat × A. glael crossing program, a genetically stable translocation line, WT153397, was developed. Sequential in situ hybridizations (McGISH) with J-, St-, and D-genomic DNA probes and pSc119.2, Afa family, pTa71, and (GAA)7 DNA repeats, as well as molecular markers specific for the wheat 6D chromosome, revealed the presence of a 6DS.6Jvs Robertsonian translocation in the genetic line. Field trials in low-input and high-input breeding nurseries over four growing seasons demonstrated the Agropyron chromosome arm's high compensating ability for the missing 6DL, as spike morphology and fertility of WT153397 did not differ significantly from those of wheat parents, Mv9kr1 and 'Mv Karizma.' Moreover, the introgressed 6Jvs chromosome arm significantly increased the number of productive tillers, resulting in a significantly higher grain yield potential compared to the parental wheat cultivars. The translocated chromosome could be highly purified by flow cytometric sorting due to the intense fluorescent labeling of (GAA)7 clusters on the Thinopyrum chromosome arm, providing an opportunity to use chromosome genomics to identify Agropyron gene variant(s) responsible for the tillering capacity. The translocation line WT153397 is an important genetic stock for functional genetic studies of tiller formation and useful breeding material for increasing wheat yield potential. The study also discusses the use of the translocation line in wheat breeding. Supplementary information The online version contains supplementary material available at 10.1007/s11032-024-01439-y.
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Affiliation(s)
- Edina Türkösi
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Éva Szakács
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - László Ivanizs
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - András Farkas
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Eszter Gaál
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Mahmoud Said
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, 779 00 Olomouc, Czechia
- Agricultural Research Centre, Field Crops Research Institute, Cairo, Egypt
| | - Éva Darkó
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Mónika Cséplő
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Péter Mikó
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Jaroslav Doležel
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, 779 00 Olomouc, Czechia
| | - Márta Molnár-Láng
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - István Molnár
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Klaudia Kruppa
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
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Kroupin PY, Yurkina AI, Ulyanov DS, Karlov GI, Divashuk MG. Comparative Characterization of Pseudoroegneria libanotica and Pseudoroegneria tauri Based on Their Repeatome Peculiarities. PLANTS (BASEL, SWITZERLAND) 2023; 12:4169. [PMID: 38140496 PMCID: PMC10747672 DOI: 10.3390/plants12244169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/05/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023]
Abstract
Pseudoroegneria species play an important role among Triticeae grasses, as they are the putative donors of the St genome in many polyploid species. Satellite repeats are widely used as a reliable tool for tracking evolutionary changes because they are distributed throughout the genomes of plants. The aim of our work is to perform a comparative characterization of the repeatomes of the closely related species Ps. libanotica and Ps. tauri, and Ps. spicata was also included in the analysis. The overall repeatome structures of Ps. libanotica, Ps. tauri, and Ps. spicata were similar, with some individual peculiarities observed in the abundance of the SIRE (Ty1/Copia) retrotransposons, Mutator and Harbinger transposons, and satellites. Nine new satellite repeats that have been identified from the whole-genome sequences of Ps. spicata and Ps. tauri, as well as the CL244 repeat that was previously found in Aegilops crassa, were localized to the chromosomes of Ps. libanotica and Ps. tauri. Four satellite repeats (CL69, CL101, CL119, CL244) demonstrated terminal and/or distal localization, while six repeats (CL82, CL89, CL168, CL185, CL192, CL207) were pericentromeric. Based on the obtained results, it can be assumed that Ps. libanotica and Ps. tauri are closely related species, although they have individual peculiarities in their repeatome structures and patterns of satellite repeat localization on chromosomes. The evolutionary fate of the identified satellite repeats and their related sequences, as well as their distribution on the chromosomes of Triticeae species, are discussed. The newly developed St genome chromosome markers developed in the present research can be useful in population studies of Ps. libanotica and Ps. tauri; auto- and allopolyploids that contain the St genome, such as Thinopyrum, Elymus, Kengyilia, and Roegneria; and wide hybrids between wheat and related wild species.
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Affiliation(s)
- Pavel Yu. Kroupin
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya St., 42, 127550 Moscow, Russia (D.S.U.)
| | - Anna I. Yurkina
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya St., 42, 127550 Moscow, Russia (D.S.U.)
| | - Daniil S. Ulyanov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya St., 42, 127550 Moscow, Russia (D.S.U.)
| | - Gennady I. Karlov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya St., 42, 127550 Moscow, Russia (D.S.U.)
| | - Mikhail G. Divashuk
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya St., 42, 127550 Moscow, Russia (D.S.U.)
- Federal Research Center “Nemchinovka”, Bolshoi Blvd., 30 Bld. 1, Skolkovo Innovation Center, 121205 Moscow, Russia
- National Research Center “Kurchatov Institute”, Kurchatov Sq., 1, 123182 Moscow, Russia
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Qi F, Liang S, Xing P, Bao Y, Wang RRC, Li X. Genome Analysis of Thinopyrum intermedium and Its Potential Progenitor Species Using Oligo-FISH. PLANTS (BASEL, SWITZERLAND) 2023; 12:3705. [PMID: 37960061 PMCID: PMC10650893 DOI: 10.3390/plants12213705] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/13/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023]
Abstract
The genome composition of intermediate wheatgrass (IWG) is complex and continues to be a subject of investigation. In this study, molecular cytogenetics were used to investigate the karyotype composition of Th. intermedium and its relative diploid species. St2-80 developed from Pseudowroegneria strigose and pDb12H developed from Dasypyrum breviaristatum were used as probes in fluorescence in situ hybridization (FISH) to classify the chromosomes of Th. intermedium into three groups, expressed as JvsJvsJrJrStSt. A combined multiplex oligonucleotide probe, including pSc119.2-1, (GAA)10, AFA-3, AFA-4, pAs1-1, Pas1-3, pAs1-4, and pAs1-6, was used to establish the FISH karyotype of ten accessions of Th. intermedium. Variability among and within the studied accessions of intermediate wheatgrass was observed in their FISH patterns. Results of this study led to the conclusions that Jvs had largely been contributed from Da. breviaristatum, but not the present-day Da. villosum; IWG had only one J genome, Jr, which was related to either Th. elongatum or Th. bessarabicum; and St was contributed from the genus Pseudoroegneria by hybridization with Th. junceiforme or Th. sartorii.
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Affiliation(s)
- Fei Qi
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (F.Q.); (P.X.); (Y.B.)
| | - Shuang Liang
- Agronomy College, Shandong Agricultural University, Tai’an 271018, China
| | - Piyi Xing
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (F.Q.); (P.X.); (Y.B.)
- Agronomy College, Shandong Agricultural University, Tai’an 271018, China
| | - Yinguang Bao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (F.Q.); (P.X.); (Y.B.)
- Agronomy College, Shandong Agricultural University, Tai’an 271018, China
| | - Richard R.-C. Wang
- USDA-ARS Forage & Range Research Laboratory (FRRL), Logan, UT 84322-6300, USA
| | - Xingfeng Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (F.Q.); (P.X.); (Y.B.)
- Agronomy College, Shandong Agricultural University, Tai’an 271018, China
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Liu Y, Song W, Song A, Wu C, Ding J, Yu X, Song J, Liu M, Yang X, Jiang C, Zhao H, Song W, Liu D, Yang X, Song Q, Li X, Cui L, Li H, Zhang Y. The improvement of agronomic performances in the cold weather conditions for perennial wheatgrass by crossing Thinopyrum intermedium with wheat- Th. intermedium partial amphiploids. FRONTIERS IN PLANT SCIENCE 2023; 14:1207078. [PMID: 37915509 PMCID: PMC10617182 DOI: 10.3389/fpls.2023.1207078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/30/2023] [Indexed: 11/03/2023]
Abstract
Thinopyrum intermedium (2n=6x=42, StStJrJrJvsJvs) is resistant or tolerant to biotic and abiotic stresses, making it suitable for developing perennial crops and forage. Through five cycles of selection, we developed 24 perennial wheatgrass lines, designated 19HSC-Q and 20HSC-Z, by crossing wheat-Th. intermedium partial amphiploids with Th. intermedium. The cold resistance, morphological performance, chromosome composition, and yield components of these perennial lines were investigated from 2019 to 2022. Six lines of 19HSC-Q had higher 1,000-kernel weight, grains per spike, and tiller number than Th. intermedium, as well as surviving -30°C in winter. Lines 19HSC-Q14, 19HSC-Q18, and 19HSC-Q20 had the best performances for grain number per spike and 1,000-kernel weight. The 20HSC-Z lines, 20HSC-Z1, 20HSC-Z2, and 20HSC-Z3, were able to survive in the cold winter in Harbin and had been grown for two years. Sequential multicolor GISH analysis revealed that the Jvs subgenome of Th. intermedium were divided into two karyotypes, three pairs of type-I Jvs chromosomes and four pairs of type-II Jvs chromosomes. Both Th. intermedium and the 24 advanced perennial wheatgrass lines had similar chromosome compositions, but the translocations among subgenome chromosomes were detected in some lines with prominent agronomic traits, such as 19HSC-Q11, 19HSC-Q14, 19HSC-Q18, 19HSC-Q20, and the three 20HSC-Z lines. The chromosome aberrations were distinguished into two types: the large fragment translocation with St-Jr, Jvs-St, Jr-IIJvs, and Jvs-Jr and the small fragment introgression of Jr-St, St-IJvs, and Jvs-Jr. These chromosomal variations can be used to further analyze the relationship between the subgenomes and phenotypes of Th. intermedium. The results of this study provide valuable materials for the next selection cycle of cold-resistant perennial wheatgrass.
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Affiliation(s)
- Yizhuo Liu
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Weiwei Song
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Anning Song
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Chunfei Wu
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Jiarui Ding
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Xiaoning Yu
- Administrative Security Division, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Jia Song
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Miaomiao Liu
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Xinyuan Yang
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Changtong Jiang
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Haibin Zhao
- Institute of Pratacultural Science, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Weifu Song
- Crop Resources Institute, Heilongjiang Academy of Agriculture Sciences, Harbin, China
| | - Dongjun Liu
- Crop Resources Institute, Heilongjiang Academy of Agriculture Sciences, Harbin, China
| | - Xuefeng Yang
- Crop Resources Institute, Heilongjiang Academy of Agriculture Sciences, Harbin, China
| | - Qingjie Song
- Crop Resources Institute, Heilongjiang Academy of Agriculture Sciences, Harbin, China
| | - Xinling Li
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Lei Cui
- College of Agriculture, Shanxi Agricultural University, Taiyuan, China
| | - Hongjie Li
- National Engineering Laboratory for Crop Molecular Breeding/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanming Zhang
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, China
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Wang S, Wang C, Feng X, Zhao J, Deng P, Wang Y, Zhang H, Liu X, Li T, Chen C, Wang B, Ji W. Molecular cytogenetics and development of St-chromosome-specific molecular markers of novel stripe rust resistant wheat-Thinopyrum intermedium and wheat-Thinopyrum ponticum substitution lines. BMC PLANT BIOLOGY 2022; 22:111. [PMID: 35279089 PMCID: PMC8917741 DOI: 10.1186/s12870-022-03496-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/24/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Owing to their excellent resistance to abiotic and biotic stress, Thinopyrum intermedium (2n = 6x = 42, JJJsJsStSt) and Th. ponticum (2n = 10x = 70) are both widely utilized in wheat germplasm innovation programs. Disomic substitution lines (DSLs) carrying one pair of alien chromosomes are valuable bridge materials for transmission of novel genes, fluorescence in situ hybridization (FISH) karyotype construction and specific molecular marker development. RESULTS Six wheat-Thinopyrum DSLs derived from crosses between Abbondanza nullisomic lines (2n = 40) and two octoploid Trititrigia lines (2n = 8x = 56), were characterized by sequential FISH-genome in situ hybridization (GISH), multicolor GISH (mc-GISH), and an analysis of the wheat 15 K SNP array combined with molecular marker selection. ES-9 (DS2St (2A)) and ES-10 (DS3St (3D)) are wheat-Th. ponticum DSLs, while ES-23 (DS2St (2A)), ES-24 (DS3St (3D)), ES-25(DS2St (2B)), and ES-26 (DS2St (2D)) are wheat-Th. intermedium DSLs. ES-9, ES-23, ES-25 and ES-26 conferred high thousand-kernel weight and stripe rust resistance at adult stages, while ES-10 and ES-24 were highly resistant to stripe rust at all stages. Furthermore, cytological analysis showed that the alien chromosomes belonging to the same homoeologous group (2 or 3) derived from different donors carried the same FISH karyotype and could form a bivalent. Based on specific-locus amplified fragment sequencing (SLAF-seq), two 2St-chromosome-specific markers (PTH-005 and PTH-013) and two 3St-chromosome-specific markers (PTH-113 and PTH-135) were developed. CONCLUSIONS The six wheat-Thinopyrum DSLs conferring stripe rust resistance can be used as bridging parents for transmission of valuable resistance genes. The utility of PTH-113 and PTH-135 in a BC1F2 population showed that the newly developed markers could be useful tools for efficient identification of St chromosomes in a common wheat background.
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Affiliation(s)
- Siwen Wang
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Changyou Wang
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100 Shaanxi China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100 Shaanxi China
| | - Xianbo Feng
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Jixin Zhao
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100 Shaanxi China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100 Shaanxi China
| | - Pingchuan Deng
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100 Shaanxi China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100 Shaanxi China
| | - Yajuan Wang
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100 Shaanxi China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100 Shaanxi China
| | - Hong Zhang
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100 Shaanxi China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100 Shaanxi China
| | - Xinlun Liu
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100 Shaanxi China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100 Shaanxi China
| | - Tingdong Li
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100 Shaanxi China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100 Shaanxi China
| | - Chunhuan Chen
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100 Shaanxi China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100 Shaanxi China
| | - Baotong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100 Shaanxi China
- College of Plant Protection, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Wanquan Ji
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100 Shaanxi China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100 Shaanxi China
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Wang H, Cheng S, Shi Y, Zhang S, Yan W, Song W, Yang X, Song Q, Jang B, Qi X, Li X, Friebe B, Zhang Y. Molecular cytogenetic characterization and fusarium head blight resistance of five wheat-Thinopyrum intermedium partial amphiploids. Mol Cytogenet 2021; 14:15. [PMID: 33676531 PMCID: PMC7937273 DOI: 10.1186/s13039-021-00536-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/19/2021] [Indexed: 11/10/2022] Open
Abstract
Background Partial amphiploids created by crossing octoploid tritelytrigia(2n = 8× = 56, AABBDDEE) and Thinopyrum intermedium (2n = 6× = 42, StStJJJSJS) are important intermediates in wheat breeding because of their resistance to major wheat diseases. We examined the chromosome compositions of five wheat-Th. intermedium partial amphiploids using GISH and multicolor-FISH. Results The result revealed that five lines had 10-14 J-genome chromosomes from Th. intermedium and 42 common wheat chromosomes, using the J-genomic DNA from Th. bessarabicum as GISH probe and the oligo probes pAs1-1, pAs1-3, AFA-4, (GAA) 10, and pSc119.2-1 as FISH probe. Five lines resembled their parent octoploid tritelytrigia (2n = 8× = 56, AABBDDEE) but had higher protein contents. Protein contents of two lines HS2-2 and HS2-5 were up to more than 20%. Evaluation of Fusarium head blight (FHB) resistance revealed that the percent of symptomatic spikelets (PSS) of these lines were below 30%. Lines HS2-2, HS2-4, HS2-5, and HS2-16 were less than 20% of PPS. Line HS2-5 with 14 J-genome chromosomes from Th. intermedium showed the best disease resistance, with PSS values of 10.8% and 16.6% in 2016 and 2017, respectively. Conclusions New wheat-Th. intermedium amphiploids with the J-genome chromosomes were identified and can be considered as a valuable source of FHB resistance in wheat breeding.
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Affiliation(s)
- Hui Wang
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, 150025, China
| | - Shuwei Cheng
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, 150025, China
| | - Yue Shi
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, 150025, China
| | - Shuxin Zhang
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, 150025, China
| | - Wei Yan
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, 150025, China
| | - Weifu Song
- Crop Resources Institute, Heilongjiang Academy of Agriculture Sciences, Harbin, 150086, China
| | - Xuefeng Yang
- Crop Resources Institute, Heilongjiang Academy of Agriculture Sciences, Harbin, 150086, China
| | - Qingjie Song
- Crop Resources Institute, Heilongjiang Academy of Agriculture Sciences, Harbin, 150086, China
| | - Bo Jang
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, 150025, China
| | - Xiaoyue Qi
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, 150025, China
| | - Xinling Li
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, 150025, China
| | - Bernd Friebe
- Department of Plant Pathology, Wheat Genetics Resource Center, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Yanming Zhang
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, 150025, China.
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Cui Y, Xing P, Qi X, Bao Y, Wang H, Wang RRC, Li X. Characterization of chromosome constitution in three wheat - Thinopyrum intermedium amphiploids revealed frequent rearrangement of alien and wheat chromosomes. BMC PLANT BIOLOGY 2021; 21:129. [PMID: 33663390 PMCID: PMC7931331 DOI: 10.1186/s12870-021-02896-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 02/21/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Thinopyrum intermedium (2n = 6x = 42) is an important wild perennial Triticeae species exhibiting many potentially favorable traits for wheat improvement. Wheat-Th. intermedium partial amphiploids serve as a bridge to transfer desirable genes from Th. intermedium into common wheat. RESULTS Three octoploid Trititrigia accessions (TE261-1, TE266-1, and TE346-1) with good resistances to stripe rust, powdery mildew and aphids were selected from hybrid progenies between Th. intermedium and the common wheat variety 'Yannong 15' (YN15). Genomic in situ hybridization (GISH), fluorescence in situ hybridization (FISH) and multicolor GISH (McGISH) analyses demonstrated that the three octoploid Trititrigia possess 42 wheat chromosomes and 14 Th. intermedium chromosomes. The 14 alien (Th. intermedium) chromosomes belong to a mixed genome consisting of J-, JS- and St-genome chromosomes rather than a single J, JS or St genome. Different types of chromosomal structural variation were also detected in the 1A, 6A, 6B, 2D and 7D chromosomes via FISH, McGISH and molecular marker analysis. The identity of the alien chromosomes and the variationes in the wheat chromosomes in the three Trititrigia octoploids were also different. CONCLUSIONS The wheat-Th. intermedium partial amphiploids possess 14 alien chromosomes which belong to a mixed genome consisting of J-, JS- and St- chromosomes, and 42 wheat chromosomes with different structural variations. These accessions could be used as genetic resources in wheat breeding for the transfer of disease and pest resistance genes from Th. intermedium to common wheat.
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Affiliation(s)
- Yu Cui
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agriculture University, Tai'an, 271018, Shandong, China
| | - Piyi Xing
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agriculture University, Tai'an, 271018, Shandong, China
| | - Xiaolei Qi
- Tai'an Academy of Agricultural Science, Tai'an, 271000, China
| | - Yinguang Bao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agriculture University, Tai'an, 271018, Shandong, China
| | - Honggang Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agriculture University, Tai'an, 271018, Shandong, China
| | - Richard R-C Wang
- USDA-ARS Forage & Range Research Laboratory, Logan, UT, 84322-6300, USA
| | - Xingfeng Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agriculture University, Tai'an, 271018, Shandong, China.
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8
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Crain J, Larson S, Dorn K, Hagedorn T, DeHaan L, Poland J. Sequenced-based paternity analysis to improve breeding and identify self-incompatibility loci in intermediate wheatgrass (Thinopyrum intermedium). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:3217-3233. [PMID: 32785739 PMCID: PMC7547974 DOI: 10.1007/s00122-020-03666-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 08/03/2020] [Indexed: 05/28/2023]
Abstract
KEY MESSAGE Paternity assignment and genome-wide association analyses for fertility were applied to a Thinopyrum intermedium breeding program. A lack of progeny between combinations of parents was associated with loci near self-incompatibility genes. In outcrossing species such as intermediate wheatgrass (IWG, Thinopyrum intermedium), polycrossing is often used to generate novel recombinants through each cycle of selection, but it cannot track pollen-parent pedigrees and it is unknown how self-incompatibility (SI) genes may limit the number of unique crosses obtained. This study investigated the potential of using next-generation sequencing to assign paternity and identify putative SI loci in IWG. Using a reference population of 380 individuals made from controlled crosses of 64 parents, paternity was assigned with 92% agreement using Cervus software. Using this approach, 80% of 4158 progeny (n = 3342) from a polycross of 89 parents were assigned paternity. Of the 89 pollen parents, 82 (92%) were represented with 1633 unique full-sib families representing 42% of all potential crosses. The number of progeny per successful pollen parent ranged from 1 to 123, with number of inflorescences per pollen parent significantly correlated to the number of progeny (r = 0.54, p < 0.001). Shannon's diversity index, assessing the total number and representation of families, was 7.33 compared to a theoretical maximum of 8.98. To test our hypothesis on the impact of SI genes, a genome-wide association study of the number of progeny observed from the 89 parents identified genetic effects related to non-random mating, including marker loci located near putative SI genes. Paternity testing of polycross progeny can impact future breeding gains by being incorporated in breeding programs to optimize polycross methodology, maintain genetic diversity, and reveal genetic architecture of mating patterns.
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Affiliation(s)
- Jared Crain
- Department of Plant Pathology, 4024 Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506, USA
| | - Steve Larson
- USDA-ARS, Forage and Range Research, Utah State University, Logan, UT, 84322, USA
| | - Kevin Dorn
- Department of Plant Pathology, 4024 Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506, USA
- USDA-ARS, Soil Management and Sugarbeet Research, Fort Collins, CO, 80526, USA
| | - Traci Hagedorn
- AAAS Science and Technology Policy Fellow, USDA-APHIS, 4700 River Road, Riverdale, MD, 20737, USA
- Quantitative Scientific Solutions LLC, Arlington, VA, 22203, USA
| | - Lee DeHaan
- The Land Institute, 2440 E. Water Well Rd, Salina, KS, 67401, USA
| | - Jesse Poland
- Department of Plant Pathology, 4024 Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506, USA.
- Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, 66506, USA.
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9
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Wang RRC, Li X, Robbins MD, Larson SR, Bushman SB, Jones TA, Thomas A. DNA sequence-based mapping and comparative genomics of the St genome of Pseudoroegneria spicata (Pursh) Á. Löve versus wheat ( Triticum aestivum L.) and barley ( Hordeum vulgare L.). Genome 2020; 63:445-457. [PMID: 32384249 DOI: 10.1139/gen-2019-0152] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bluebunch wheatgrass (referred to as BBWG) [Pseudoroegneria spicata (Pursh) Á. Löve] is an important rangeland Triticeae grass used for forage, conservation, and restoration. This diploid has the basic St genome that occurs also in many polyploid Triticeae species, which serve as a gene reservoir for wheat improvement. Until now, the St genome in diploid species of Pseudoroegneria has not been mapped. Using a double-cross mapping populations, we mapped 230 expressed sequence tag derived simple sequence repeat (EST-SSR) and 3468 genotyping-by-sequencing (GBS) markers to 14 linkage groups (LGs), two each for the seven homologous groups of the St genome. The 227 GBS markers of BBWG that matched those in a previous study helped identify the unclassified seven LGs of the St sub-genome among 21 LGs of Thinopyrum intermedium (Host) Barkworth & D.R. Dewey. Comparisons of GBS sequences in BBWG to whole-genome sequences in bread wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) revealed that the St genome shared a homology of 35% and 24%, a synteny of 86% and 84%, and a collinearity of 0.85 and 0.86, with ABD and H, respectively. This first-draft molecular map of the St genome will be useful in breeding cereal and forage crops.
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Affiliation(s)
- Richard R-C Wang
- U.S. Department of Agriculture, Agricultural Research Service, Forage and Range Research Laboratory, Utah State University, Logan, UT 84322-6300, USA
| | - Xingfeng Li
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Matthew D Robbins
- U.S. Department of Agriculture, Agricultural Research Service, Forage and Range Research Laboratory, Utah State University, Logan, UT 84322-6300, USA
| | - Steve R Larson
- U.S. Department of Agriculture, Agricultural Research Service, Forage and Range Research Laboratory, Utah State University, Logan, UT 84322-6300, USA
| | - Shaun B Bushman
- U.S. Department of Agriculture, Agricultural Research Service, Forage and Range Research Laboratory, Utah State University, Logan, UT 84322-6300, USA
| | - Thomas A Jones
- U.S. Department of Agriculture, Agricultural Research Service, Forage and Range Research Laboratory, Utah State University, Logan, UT 84322-6300, USA
| | - Aaron Thomas
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT 84322-4815, USA
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10
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Divashuk MG, Karlov GI, Kroupin PY. Copy Number Variation of Transposable Elements in Thinopyrum intermedium and Its Diploid Relative Species. PLANTS 2019; 9:plants9010015. [PMID: 31877707 PMCID: PMC7020174 DOI: 10.3390/plants9010015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/05/2019] [Accepted: 12/17/2019] [Indexed: 12/14/2022]
Abstract
Diploid and polyploid wild species of Triticeae have complex relationships, and the understanding of their evolution and speciation could help to increase the usability of them in wheat breeding as a source of genetic diversity. The diploid species Pseudoroegneria spicata (St), Thinopyrum bessarabicum (Jb), Dasypyrum villosum (V) derived from a hypothetical common ancestor are considered to be possible subgenome donors in hexaploid species Th. intermedium (JrJvsSt, where indices r, v, and s stand for the partial relation to the genomes of Secale, Dasypyrum, and Pseudoroegneria, respectively). We quantified 10 families of transposable elements (TEs) in P. spicata, Th. bessarabicum, D. villosum (per one genome), and Th. intermedium (per one average subgenome) using the quantitative real time PCR assay and compared their abundance within the studied genomes as well as between them. Sabrina was the most abundant among all studied elements in P. spicata, D. villosum, and Th. intermedium, and among Ty3/Gypsy elements in all studied species. Among Ty1/Copia elements, Angela-A and WIS-A showed the highest and close abundance with the exception of D. villosum, and comprised the majority of all studied elements in Th. bessarabicum. Sabrina, BAGY2, and Angela-A showed similar abundance among diploids and in Th. intermedium hexaploid; Latidu and Barbara demonstrated sharp differences between diploid genomes. The relationships between genomes of Triticeae species based on the studied TE abundance and the role of TEs in speciation and polyploidization in the light of the current phylogenetic models is discussed.
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Affiliation(s)
- Mikhail G. Divashuk
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow 127550, Russia; (M.G.D.)
- Centre for Molecular Biotechnology, Russian State Agrarian University-Timiryazev Agricultural Academy, Moscow 127550, Russia
| | - Gennady I. Karlov
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow 127550, Russia; (M.G.D.)
- Centre for Molecular Biotechnology, Russian State Agrarian University-Timiryazev Agricultural Academy, Moscow 127550, Russia
| | - Pavel Yu. Kroupin
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow 127550, Russia; (M.G.D.)
- Centre for Molecular Biotechnology, Russian State Agrarian University-Timiryazev Agricultural Academy, Moscow 127550, Russia
- Correspondence:
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11
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Cseh A, Yang C, Hubbart-Edwards S, Scholefield D, Ashling SS, Burridge AJ, Wilkinson PA, King IP, King J, Grewal S. Development and validation of an exome-based SNP marker set for identification of the St, J r and J vs genomes of Thinopyrym intermedium in a wheat background. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1555-1570. [PMID: 30767030 PMCID: PMC6476854 DOI: 10.1007/s00122-019-03300-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 02/02/2019] [Indexed: 05/19/2023]
Abstract
KEY MESSAGE Cytogenetic analysis and array-based SNP genotyping of wheat- Th. intermedium introgression lines allowed identification of 634 chromosome-specific SNP markers across all twenty-one chromosomes of Th. intermedium (StJ r J vs , 2 n = 6 x = 42). Thinopyrum intermedium (2n = 6x = 42, StJrJvs) is one of the most promising reservoirs of useful genes including tolerance to abiotic stresses, perenniality and disease resistance not available in the cultivated bread wheat. The transfer of genetic diversity from wild species to wheat offers valuable responses to the effects of climate change. The new array-based single-nucleotide polymorphism (SNP) marker technology provides cheap and easy-to-use molecular markers for marker-assisted selection (MAS) in wheat breeding programmes. Here, we focus on the generation of a new chromosome-specific SNP marker set that can be used to characterize and identify the Th. intermedium chromosomes or chromosome segments transferred into wheat. A progressive investigation of marker development was conducted using 187 various newly developed wheat-Th. intermedium introgression lines and the Axiom® Wheat-Relative Genotyping array. We employed molecular cytogenetic techniques to clarify the genome constitution of the Th. intermedium parental lines and validated 634 chromosome-specific SNPs. Our data confirmed the allohexaploid nature of Th. intermedium and demonstrated that the St genome-specific GISH signal and markers are present at the centromeric regions of chromosomes 1Jvs, 2Jvs, 3Jvs and 7Jvs. The SNP markers presented here will be introduced into current wheat improvement programmes, offering a significant speed-up in wheat breeding and making it possible to deal with the transfer of the full genetic potential of Th. intermedium into wheat.
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Affiliation(s)
- Andras Cseh
- Nottingham BBSRC Wheat Research Centre, Division of Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, UK
- Molecular Breeding Department, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Caiyun Yang
- Nottingham BBSRC Wheat Research Centre, Division of Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Stella Hubbart-Edwards
- Nottingham BBSRC Wheat Research Centre, Division of Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Duncan Scholefield
- Nottingham BBSRC Wheat Research Centre, Division of Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Stephen S Ashling
- Nottingham BBSRC Wheat Research Centre, Division of Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | | | | | - Ian P King
- Nottingham BBSRC Wheat Research Centre, Division of Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Julie King
- Nottingham BBSRC Wheat Research Centre, Division of Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Surbhi Grewal
- Nottingham BBSRC Wheat Research Centre, Division of Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, UK.
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12
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Cui Y, Zhang Y, Qi J, Wang H, Wang RRC, Bao Y, Li X. Identification of chromosomes in Thinopyrum intermedium and wheat Th. intermedium amphiploids based on multiplex oligonucleotide probes. Genome 2018; 61:515-521. [DOI: 10.1139/gen-2018-0019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Synthesized oligonucleotides (oligos) can be used as effective probes similar to plasmid clones for chromosome identification in fluorescence in situ hybridization (FISH) analysis, making oligo FISH a simpler and more efficient molecular cytogenetic technique for studying plants. In this study, multiplex oligonucleotide probes, including pSc119.2-1, pAs1-4, (GAA)10, (AAC)6, and pTa71, were combined and used in FISH to identify chromosomes in common wheat, Thinopyrum intermedium, and a wheat – Th. intermedium amphiploid TE256-1. In comparison with general FISH probes, signals generated by the multiplex probes were more abundant, colorful, and characteristic. Combining the results of genomic in situ hybridization (GISH) with FISH, Th. intermedium chromosomes and alien chromosomes in TE256-1 could be classified and identified more precisely, especially the J- and Js-genome chromosomes. Moreover, based on the FISH results using multiplex probes, more structural variations in wheat chromosomes of TE256-1 were detected. The results indicated that multiplex oligo probes would have a wide range of application prospects in the creation and identification of wheat – Th. intermedium germplasms.
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Affiliation(s)
- Yu Cui
- State Key Laboratory of Crop Biology, Shandong Agriculture University, Tai’an, Shandong 271018, China
| | - Yanping Zhang
- College of Agronomy, Shandong Agriculture University, Tai’an, Shandong 271018, China
| | - Juan Qi
- State Key Laboratory of Crop Biology, Shandong Agriculture University, Tai’an, Shandong 271018, China
| | - Honggang Wang
- State Key Laboratory of Crop Biology, Shandong Agriculture University, Tai’an, Shandong 271018, China
- College of Agronomy, Shandong Agriculture University, Tai’an, Shandong 271018, China
| | - Richard R.-C. Wang
- United States Department of Agriculture – Agricultural Research Services, Forage and Range Research Laboratory, Logan, UT 84322-6300, USA
| | - Yinguang Bao
- College of Agronomy, Shandong Agriculture University, Tai’an, Shandong 271018, China
| | - Xingfeng Li
- State Key Laboratory of Crop Biology, Shandong Agriculture University, Tai’an, Shandong 271018, China
- College of Agronomy, Shandong Agriculture University, Tai’an, Shandong 271018, China
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13
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Liu L, Luo Q, Teng W, Li B, Li H, Li Y, Li Z, Zheng Q. Development of Thinopyrum ponticum-specific molecular markers and FISH probes based on SLAF-seq technology. PLANTA 2018; 247:1099-1108. [PMID: 29356894 DOI: 10.1007/s00425-018-2845-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/07/2018] [Indexed: 05/06/2023]
Abstract
Based on SLAF-seq, 67 Thinopyrum ponticum-specific markers and eight Th. ponticum-specific FISH probes were developed, and these markers and probes could be used for detection of alien chromatin in a wheat background. Decaploid Thinopyrum ponticum (2n = 10x = 70) is a valuable gene reservoir for wheat improvement. Identification of Th. ponticum introgression would facilitate its transfer into diverse wheat genetic backgrounds and its practical utilization in wheat improvement. Based on specific-locus-amplified fragment sequencing (SLAF-seq) technology, 67 new Th. ponticum-specific molecular markers and eight Th. ponticum-specific fluorescence in situ hybridization (FISH) probes have been developed from a tiny wheat-Th. ponticum translocation line. These newly developed molecular markers allowed the detection of Th. ponticum DNA in a variety of materials specifically and steadily at high throughput. According to the hybridization signal pattern, the eight Th. ponticum-specific probes could be divided into two groups. The first group including five dispersed repetitive sequence probes could identify Th. ponticum chromatin more sensitively and accurately than genomic in situ hybridization (GISH). Whereas the second group having three tandem repetitive sequence probes enabled the discrimination of Th. ponticum chromosomes together with another clone pAs1 in wheat-Th. ponticum partial amphiploid Xiaoyan 68.
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Affiliation(s)
- Liqin Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences/State Key Laboratory of Plant Cell and Chromosome Engineering, Beijing, 100101, China
| | - Qiaoling Luo
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences/State Key Laboratory of Plant Cell and Chromosome Engineering, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wan Teng
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences/State Key Laboratory of Plant Cell and Chromosome Engineering, Beijing, 100101, China
| | - Bin Li
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences/State Key Laboratory of Plant Cell and Chromosome Engineering, Beijing, 100101, China
| | - Hongwei Li
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences/State Key Laboratory of Plant Cell and Chromosome Engineering, Beijing, 100101, China
| | - Yiwen Li
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences/State Key Laboratory of Plant Cell and Chromosome Engineering, Beijing, 100101, China
| | - Zhensheng Li
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences/State Key Laboratory of Plant Cell and Chromosome Engineering, Beijing, 100101, China.
| | - Qi Zheng
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences/State Key Laboratory of Plant Cell and Chromosome Engineering, Beijing, 100101, China.
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14
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Phylogenetic relationships of ascomycetes and basidiomycetes based on comparative genomics analysis. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0595-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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15
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Wang RRC, Larson SR, Jensen KB. Differential transferability of EST-SSR primers developed from the diploid species Pseudoroegneria spicata, Thinopyrum bessarabicum, and Thinopyrum elongatum. Genome 2017; 60:530-536. [PMID: 28235186 DOI: 10.1139/gen-2016-0157] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Simple sequence repeat technology based on expressed sequence tag (EST-SSR) is a useful genomic tool for genome mapping, characterizing plant species relationships, elucidating genome evolution, and tracing genes on alien chromosome segments. EST-SSR primers developed from three perennial diploid species of Triticeae, Pseudoroegneria spicata (Pursh) Á. Löve (having St genome), Thinopyrum bessarabicum (Savul. & Rayss) Á. Löve (Jb = Eb = J), and Thinopyrum elongatum (Host) D.R. Dewey (Je = Ee = E), were used to produce amplicons in these three species to (i) assess relative transferability, (ii) identify polymorphic species-specific markers, and (iii) determine genome relationships among the three species. Because of the close relationship between Jb and Je genomes, EST-SSR primers derived from Th. bessarabicum and Th. elongatum had greater transferability to each other than those derived from the St-genome P. spicata. A large number of polymorphic species- and genome-specific EST-SSR amplicons were identified that will be used for construction of genetic maps of these diploid species, and tracing economically useful genes in breeding or gene transfer programs in various species of Triticeae.
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Affiliation(s)
- Richard R-C Wang
- United States Department of Agriculture - Agricultural Research Services Forage and Range Research Laboratory, Logan, UT 84322-6300, USA.,United States Department of Agriculture - Agricultural Research Services Forage and Range Research Laboratory, Logan, UT 84322-6300, USA
| | - Steve R Larson
- United States Department of Agriculture - Agricultural Research Services Forage and Range Research Laboratory, Logan, UT 84322-6300, USA.,United States Department of Agriculture - Agricultural Research Services Forage and Range Research Laboratory, Logan, UT 84322-6300, USA
| | - Kevin B Jensen
- United States Department of Agriculture - Agricultural Research Services Forage and Range Research Laboratory, Logan, UT 84322-6300, USA.,United States Department of Agriculture - Agricultural Research Services Forage and Range Research Laboratory, Logan, UT 84322-6300, USA
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16
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Kantarski T, Larson S, Zhang X, DeHaan L, Borevitz J, Anderson J, Poland J. Development of the first consensus genetic map of intermediate wheatgrass (Thinopyrum intermedium) using genotyping-by-sequencing. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:137-150. [PMID: 27738715 DOI: 10.1007/s00122-016-2799-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 09/27/2016] [Indexed: 05/26/2023]
Abstract
Development of the first consensus genetic map of intermediate wheatgrass gives insight into the genome and tools for molecular breeding. Intermediate wheatgrass (Thinopyrum intermedium) has been identified as a candidate for domestication and improvement as a perennial grain, forage, and biofuel crop and is actively being improved by several breeding programs. To accelerate this process using genomics-assisted breeding, efficient genotyping methods and genetic marker reference maps are needed. We present here the first consensus genetic map for intermediate wheatgrass (IWG), which confirms the species' allohexaploid nature (2n = 6x = 42) and homology to Triticeae genomes. Genotyping-by-sequencing was used to identify markers that fit expected segregation ratios and construct genetic maps for 13 heterogeneous parents of seven full-sib families. These maps were then integrated using a linear programming method to produce a consensus map with 21 linkage groups containing 10,029 markers, 3601 of which were present in at least two populations. Each of the 21 linkage groups contained between 237 and 683 markers, cumulatively covering 5061 cM (2891 cM--Kosambi) with an average distance of 0.5 cM between each pair of markers. Through mapping the sequence tags to the diploid (2n = 2x = 14) barley reference genome, we observed high colinearity and synteny between these genomes, with three homoeologous IWG chromosomes corresponding to each of the seven barley chromosomes, and mapped translocations that are known in the Triticeae. The consensus map is a valuable tool for wheat breeders to map important disease-resistance genes within intermediate wheatgrass. These genomic tools can help lead to rapid improvement of IWG and development of high-yielding cultivars of this perennial grain that would facilitate the sustainable intensification of agricultural systems.
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Affiliation(s)
- Traci Kantarski
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton, Manhattan, KS, 66506, USA
| | - Steve Larson
- USDA-ARS, Forage and Range Research, Utah State University, Logan, UT, 84322, USA
| | - Xiaofei Zhang
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Buford Circle, St. Paul, MN, 55108, USA
| | - Lee DeHaan
- The Land Institute, 2440 E. Water Well Rd, Salina, KS, 67401, USA
| | - Justin Borevitz
- Research School of Biology, Australian National University, Canberra, Australia
| | - James Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Buford Circle, St. Paul, MN, 55108, USA
| | - Jesse Poland
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton, Manhattan, KS, 66506, USA.
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17
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Li G, Wang H, Lang T, Li J, La S, Yang E, Yang Z. New molecular markers and cytogenetic probes enable chromosome identification of wheat-Thinopyrum intermedium introgression lines for improving protein and gluten contents. PLANTA 2016; 244:865-76. [PMID: 27290728 DOI: 10.1007/s00425-016-2554-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 06/06/2016] [Indexed: 05/19/2023]
Abstract
New molecular markers were developed for targeting Thinopyrum intermedium 1St#2 chromosome, and novel FISH probe representing the terminal repeats was produced for identification of Thinopyrum chromosomes. Thinopyrum intermedium has been used as a valuable resource for improving the disease resistance and yield potential of wheat. A wheat-Th. intermedium ssp. trichophorum chromosome 1St#2 substitution and translocation has displayed superior grain protein and wet gluten content. With the aim to develop a number of chromosome 1St#2 specific molecular and cytogenetic markers, a high throughput, low-cost specific-locus amplified fragment sequencing (SLAF-seq) technology was used to compare the sequences between a wheat-Thinopyrum 1St#2 (1D) substitution and the related species Pseudoroegneria spicata (St genome, 2n = 14). A total of 5142 polymorphic fragments were analyzed and 359 different SLAF markers for 1St#2 were predicted. Thirty-seven specific molecular markers were validated by PCR from 50 randomly selected SLAFs. Meanwhile, the distribution of transposable elements (TEs) at the family level between wheat and St genomes was compared using the SLAFs. A new oligo-nucleotide probe named Oligo-pSt122 from high SLAF reads was produced for fluorescence in situ hybridization (FISH), and was observed to hybridize to the terminal region of 1St#L and also onto the terminal heterochromatic region of Th. intermedium genomes. The genome-wide markers and repetitive based probe Oligo-pSt122 will be valuable for identifying Thinopyrum chromosome segments in wheat backgrounds.
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Affiliation(s)
- Guangrong Li
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, China
| | - Hongjin Wang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, China
| | - Tao Lang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, China
| | - Jianbo Li
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, China
| | - Shixiao La
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, China
| | - Ennian Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
| | - Zujun Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, China.
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18
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Kruppa K, Molnár-Láng M. Simultaneous visualization of different genomes (J, JSt and St) in a Thinopyrum intermedium × Thinopyrum ponticum synthetic hybrid (Poaceae) and in its parental species by multicolour genomic in situ hybridization (mcGISH). COMPARATIVE CYTOGENETICS 2016; 10:283-93. [PMID: 27551349 PMCID: PMC4977803 DOI: 10.3897/compcytogen.v10i2.7305] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 04/27/2016] [Indexed: 05/19/2023]
Abstract
Multicolour genomic in situ hybridization (mcGISH) using total genomic DNA probes from Thinopyrum bessarabicum (Săvulescu & Rayss, 1923) Á. Löve, 1984 (genome J(b) or E(b), 2n = 14), and Pseudoroegneria spicata (Pursh, 1814) Á. Löve, 1980 (genome St, 2n = 14) was used to characterize the mitotic metaphase chromosomes of a synthetic hybrid of Thinopyrum intermedium (Host, 1805) Barkworth & D.R. Dewey, 1985 and Thinopyrum ponticum (Podpěra, 1902) Z.-W. Liu et R.-C.Wang, 1993 named "Agropyron glael" and produced by N.V. Tsitsin in the former Soviet Union. The mcGISH pattern of this synthetic hybrid was compared to its parental wheatgrass species. Hexaploid Thinopyrum intermedium contained 19 J, 9 J(St) and 14 St chromosomes. The three analysed Thinopyrum ponticum accessions had different chromosome compositions: 43 J + 27 J(St) (PI531737), 40 J + 30 J(St) (VIR-44486) and 38 J + 32 J(St) (D-3494). The synthetic hybrid carried 18 J, 28 J(St) and 8 St chromosomes, including one pair of J-St translocation and/or decreased fluorescent intensity, resulting in unique hybridization patterns. Wheat line Mv9kr1 was crossed with the Thinopyrum intermedium × Thinopyrum ponticum synthetic hybrid in Hungary in order to transfer its advantageous agronomic traits (leaf rust and yellow rust resistance) into wheat. The chromosome composition of a wheat/A.glael F1 hybrid was 21 wheat + 28 wheatgrass (11 J + 14 J(St)+ 3 S). In the present study, mcGISH involving the simultaneous use of St and J genomic DNA as probes provided information about the type of Thinopyrum chromosomes in a Thinopyrum intermedium/Thinopyrum ponticum synthetic hybrid called A. glael.
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Affiliation(s)
- Klaudia Kruppa
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Department of Plant Genetic Resources, H-2462 Martonvásár, Brunszvik u. 2, Hungary
| | - Márta Molnár-Láng
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Department of Plant Genetic Resources, H-2462 Martonvásár, Brunszvik u. 2, Hungary
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Variation in Copy Number of Ty3/Gypsy Centromeric Retrotransposons in the Genomes of Thinopyrum intermedium and Its Diploid Progenitors. PLoS One 2016; 11:e0154241. [PMID: 27119343 PMCID: PMC4847875 DOI: 10.1371/journal.pone.0154241] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 04/11/2016] [Indexed: 01/20/2023] Open
Abstract
Speciation and allopolyploidization in cereals may be accompanied by dramatic changes in abundance of centromeric repeated transposable elements. Here we demonstrate that the reverse transcriptase part of Ty3/gypsy centromeric retrotransposon (RT-CR) is highly conservative in the segmental hexaploid Thinopyrum intermedium (JrJvsSt) and its possible diploid progenitors Th. bessarabicum (Jb), Pseudoroegneria spicata (St) and Dasypyrum villosum (V) but the abundance of the repeats varied to a large extent. Fluorescence in situ hybridization (FISH) showed hybridization signals in centromeric region of all chromosomes in the studied species, although the intensity of the signals drastically differed. In Th. intermedium, the strongest signal of RT-CR probe was detected on the chromosomes of Jv, intermediate on Jr and faint on Js and St subgenome suggesting different abundance of RT-CR on the individual chromosomes rather than the sequence specificity of RT-CRs of the subgenomes. RT-CR quantification using real-time PCR revealed that its content per genome in Th. bessarabicum is ~ 2 times and P. spicata is ~ 1,5 times higher than in genome of D. villosum. The possible burst of Ty3/gypsy centromeric retrotransposon in Th. intermedium during allopolyploidization and its role in proper mitotic and meiotic chromosome behavior in a nascent allopolyploid is discussed.
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