1
|
Katayama K, Ito J, Murakami R, Yamashita A, Sasajima H, Narahashi S, Chiba J, Yamamoto I, Fujii W, Tochigi Y, Suzuki H. Mutation of the Thap4 gene causes dwarfism and testicular anomalies in rats and mice. Mamm Genome 2024; 35:149-159. [PMID: 38658415 DOI: 10.1007/s00335-024-10041-8] [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: 01/18/2024] [Accepted: 04/15/2024] [Indexed: 04/26/2024]
Abstract
The petit (pet) locus is associated with dwarfism, testicular anomalies, severe thymic hypoplasia, and high postnatal lethality, which are inherited in autosomal recessive mode of inheritance in rats with a Wistar strain genetic background. Linkage analysis localized the pet locus between 98.7 Mb and 101.2 Mb on rat chromosome 9. Nucleotide sequence analysis identified 2 bp deletion in exon 2 of the Thap4 gene as the causative mutation for pet. This deletion causes a frameshift and premature termination codon, resulting in a truncated THAP4 protein lacking approximately two-thirds of the C-terminal side. Thap4 is expressed in various organs, including the testis and thymus in rats. To elucidate the biological function of THAP4 in other species, we generated Thap4 knockout mice lacking exon 2 of the Thap4 gene through genome editing. Thap4 knockout mice also exhibited dwarfism and small testis but did not show high postnatal lethality. Thymus weights of adult Thap4 knockout male mice were significantly higher compared to wild-type male mice. Although Thap4 knockout male mice were fertile, their testis contained seminiferous tubules with spermatogenesis and degenerative seminiferous tubules lacking germ cells. Additionally, we observed vacuoles in seminiferous tubules, and clusters of cells in the lumen in seminiferous tubules in Thap4 knockout male mice. These results demonstrate that spontaneous mutation of Thap4 gene in rats and knockout of Thap4 gene in mice both cause dwarfism and testicular anomalies. Thap4 gene in rats and mice is essential for normal testicular development, maintaining spermatogenesis throughout the entire region of seminiferous tubules.
Collapse
Affiliation(s)
- Kentaro Katayama
- Laboratory of Veterinary Physiology, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo, 180-8602, Japan
| | - Junya Ito
- Laboratory of Veterinary Physiology, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo, 180-8602, Japan
| | - Rei Murakami
- Laboratory of Veterinary Physiology, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo, 180-8602, Japan
| | - Ayako Yamashita
- Laboratory of Veterinary Physiology, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo, 180-8602, Japan
| | - Hotaka Sasajima
- Laboratory of Veterinary Physiology, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo, 180-8602, Japan
| | - Satomi Narahashi
- Laboratory of Veterinary Physiology, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo, 180-8602, Japan
| | - Junko Chiba
- Laboratory of Veterinary Physiology, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo, 180-8602, Japan
| | - Ichiro Yamamoto
- Laboratory of Veterinary Biochemistry, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo, 180-8602, Japan
| | - Wataru Fujii
- Laboratory of Biomedical Science, Department of Veterinary Medical Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yuki Tochigi
- Laboratory of Veterinary Physiology, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo, 180-8602, Japan
| | - Hiroetsu Suzuki
- Laboratory of Veterinary Physiology, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo, 180-8602, Japan.
| |
Collapse
|
2
|
Lou X, Su J, Xiong Y, Chen M, Zhang Q, Luan Y, Sun C, Fu Y, Zhang K. Identification of QTLs responsible for culturability, and fine-mapping of QTL qCBT9 related to callus browning derived from Dongxiang common wild rice ( Oryza rufipogon Griff.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:32. [PMID: 38685957 PMCID: PMC11055834 DOI: 10.1007/s11032-024-01470-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/08/2024] [Indexed: 05/02/2024]
Abstract
Compared to japonica, the lower genetic transformation efficiency of indica is a technical bottleneck for rice molecular breeding. Specifically, callus browning frequently occurs during the culture of the elite indica variety 93-11, leading to poor culturability and lower genetic transformation efficiency. Here, 67 QTLs related to culturability were detected using 97 introgression lines (designated as 9DILs) derived from Dongxiang common wild rice (DXCWR, Oryza rufipogon Griff.) with 93-11 genetic background, explaining 4% ~12% of the phenotypic variations. The QTL qCBT9 on chromosome 9 was a primary QTL for reducing callus browning derived from DXCWR. Five 9DILs with light callus browning and high differentiation were screened. We evaluated the callus browning index (CBI) of 100 F2 population crossed of 93-11 and 9DIL71 and the recombinant plants screened from 3270 individuals. The qCBT9 was delimited to a ~148kb region between the markers X16 and X23. RNA-seq analysis of DEGs between 9DIL71 and 93-11 showed three upregulated DEGs (Os09g0526500, Os09g0527900, Os09g0528200,) and three downregulated DEGs (Os09g0526700, Os09g0526800, Os09g0527700) were located in the candidate region of qCBT9. Furthermore, callus browning may be involved in cell senescence and death caused by oxidative stress. The differentiation of indica and japonica in this region suggested that qCBT9 was possibly a vital QTL contributed to better culturability of japonica. Our results laid a foundation for further cloning of the gene for reduced callus browning in O. rufipogon, and also provided a new genetic resource and material basis for improving the culturability and genetic transformation efficiency of cultivated rice. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01470-z.
Collapse
Affiliation(s)
- Xin Lou
- National Center for Evaluation of Agricultural Wild Plants (Rice), Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193 China
| | - Jingjing Su
- National Center for Evaluation of Agricultural Wild Plants (Rice), Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193 China
| | - Yuzhu Xiong
- National Center for Evaluation of Agricultural Wild Plants (Rice), Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193 China
| | - Min Chen
- National Center for Evaluation of Agricultural Wild Plants (Rice), Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193 China
| | - Qiaowen Zhang
- Agricultural Technology Extension Center of Dunhua City, Dunhua, 133700 China
| | - Yanfang Luan
- National Center for Evaluation of Agricultural Wild Plants (Rice), Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193 China
| | - Chuanqing Sun
- National Center for Evaluation of Agricultural Wild Plants (Rice), Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193 China
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, 10093 China
| | - Yongcai Fu
- National Center for Evaluation of Agricultural Wild Plants (Rice), Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193 China
| | - Kun Zhang
- National Center for Evaluation of Agricultural Wild Plants (Rice), Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193 China
| |
Collapse
|
3
|
Taliei F, Sabouri H, Kazerani B, Ghasemi S. Finding stable and closely linked QTLs against spot blotch in different planting dates during the adult stage in barley. Sci Rep 2024; 14:818. [PMID: 38191625 PMCID: PMC10774436 DOI: 10.1038/s41598-024-51358-3] [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: 07/14/2023] [Accepted: 01/03/2024] [Indexed: 01/10/2024] Open
Abstract
The common resistance to Spot Blotch (SB) and drought stress in barley was studied using a RILs population caused Kavir × Badia cross. These lines were inoculated with Cochliobolus sativus Gonbad isolate during the adult stage and were evaluated for three crop seasons in different planting dates. The different osmotic potentials during the flowering were regulated by changing the planting dates. In total, 43 lines had resistant to SB and drought. The high-density linkage map covered 1045 cM of barley genome. A total of five stable and closely linked QTLs to SB resistance were mapped on chromosomes 2H, 3H, 4H and 7H using genome-wide composite interval mapping. Moreover, four stable and closely linked QTLs to SB susceptibility were located on chromosomes 3H, 4H, 5H and 7H. Additionally, the ISJ19-A, SCoT7-C, ISJ17-B, Bmac0144k, iPBS2415-1, Bmac0282b and EBmatc0016 markers can be used for positive screening of resistant cultivars. However, ISJ3-C, UMB310, ISJ9-B, UMB706, D03-D and iPBS2257-A markers can be used for negative screening of susceptible cultivars in marker-assisted selection. The bioinformatics studies showed that QRCsa-2H (ISJ19-A region), QRCsa-2H (SCoT7-C-ISJ17-B region), QRCsa-3H (Bmac0144k region), QRCsa-4H (iPBS2415-1 region) and QRCsa-7H (Bmac0282b-EBmatc0016 region) are involved in the carboxypeptidase, Glycosyltransferase, transcription factors, kinase and AP2/ERF, respectively.
Collapse
Affiliation(s)
- Fakhtak Taliei
- Department of Plant Production, College of Agriculture Science and Natural Resources, Gonbad Kavous University, Gonbad Kavous, Iran.
| | - Hossein Sabouri
- Department of Plant Production, College of Agriculture Science and Natural Resources, Gonbad Kavous University, Gonbad Kavous, Iran
| | - Borzo Kazerani
- Department of Plant Breeding and Biotechnology, Faculty of Plant Production, Gorgan University of Agricultural Science and Natural Resources, Gorgan, Iran
| | - Shahram Ghasemi
- Department of Plant Production, College of Agriculture Science and Natural Resources, Gonbad Kavous University, Gonbad Kavous, Iran
| |
Collapse
|
4
|
Chemayek B, Wagoire W, Bansal U, Bariana H. A Combination of Three Genomic Regions Conditions High Level of Adult Plant Stripe Rust Resistance in Australian Wheat Cultivar Sentinel. PLANTS (BASEL, SWITZERLAND) 2024; 13:129. [PMID: 38202436 PMCID: PMC10780541 DOI: 10.3390/plants13010129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/15/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024]
Abstract
A seedling susceptible Australian common wheat cultivar Sentinel showed resistance to stripe rust under field conditions. A Sentinel/Nyabing3 (Nyb3)-derived recombinant inbred line (RIL) population was phenotyped. A DArTseq marker-based linkage map of the Sentinel/Nyb3 RIL population was used to determine the chromosomal location of the adult plant stripe rust resistance possessed by Sentinel. Three consistent quantitative trait loci (QTL); QYr.sun-1BL, QYr.sun-2AS and QYr.sun-3BS were detected, and they on an average explained 18%, 15.6% and 10.6% of the variation in stripe rust response, respectively. All three QTL were contributed by Sentinel. QYr.sun-1B corresponded to the previously characterized gene Yr29. Sentinel expressed resistance at the four-leaf stage at 21 ± 2 °C in the greenhouse. Monogenic segregation among the RIL population was observed when screened at the four-leaf stage at 21 ± 2 °C in the greenhouse, and the underlying resistance locus was temporarily named YrSen. QYr.sun-3BS peaked on YrSen. QYr.sun-2AS was mendelized by generating and phenotyping a mongenically sgregating F6 RIL population, and it was temporarily designated YrSen2. RILs carrying Yr29, YrSen and YrSen2 in combination exhibited responses like the parent Sentinel. Based on a comparison of the genomic locations and resistance expression with stripe rust resistance genes previously located in their respective chromosomes, QYr.sun-2AS (YrSen2) and QYr.sun-3BS (YrSen) were concluded to represent new loci.
Collapse
Affiliation(s)
- Bosco Chemayek
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, 107 Cobbitty Road, Cobbitty, NSW 2570, Australia; (B.C.); (U.B.)
- Buginyanya Zonal Agricultural Research Institute, National Agricultural Research Organisation, Mbale P.O. Box 1356, Uganda;
| | - William Wagoire
- Buginyanya Zonal Agricultural Research Institute, National Agricultural Research Organisation, Mbale P.O. Box 1356, Uganda;
| | - Urmil Bansal
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, 107 Cobbitty Road, Cobbitty, NSW 2570, Australia; (B.C.); (U.B.)
| | - Harbans Bariana
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, 107 Cobbitty Road, Cobbitty, NSW 2570, Australia; (B.C.); (U.B.)
- School of Science, Hawkesbury Campus, Western Sydney University, Bourke Street, Richmond, NSW 2753, Australia
| |
Collapse
|
5
|
Gao P, Zhou Y, Gebrewahid TW, Zhang P, Wang S, Liu D, Li Z. QTL Mapping for Adult-Plant Resistance to Leaf Rust in Italian Wheat Cultivar Libellula. PLANT DISEASE 2024; 108:13-19. [PMID: 37526485 DOI: 10.1094/pdis-01-23-0105-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Wheat leaf rust (Lr), which is caused by Puccinia triticina Eriks. (Pt), is one of the most important wheat diseases affecting wheat production globally. Using resistant wheat cultivars is the most economical and environmentally friendly way to control leaf rust. The Italian wheat cultivar Libellula has demonstrated good resistance to Lr in field studies. To identify the genetic basis of Lr resistance in 'Libellula', 248 F6 recombinant inbred lines from the cross 'Libellula'/'Huixianhong' was phenotyped for Lr severity in seven environments: the 2014/2015, 2016/2017, 2017/2018, and 2018/2019 cropping seasons at Baoding, Hebei Province, and the 2016/2017, 2017/2018, and 2018/2019 crop seasons at Zhoukou, Henan Province. Bulked segregant analysis and simple sequence repeat markers were then used to identify the quantitative trait loci (QTLs) for Lr adult-plant resistance in the population. Six QTLs were consequently detected and designated as QLr.hebau-1AL and QLr.hebau-1AS that were presumed to be new and QLr.hebau-1BL, QLr.hebau-3AL, QLr.hebau-4BL, and QLr.hebau-7DS that were identified at similar physical positions as previously reported QTLs. Based on chromosome positions and molecular marker tests, QLr.hebau-1BL and QLr.hebau-7DS share similar flanking markers with Lr46 and Lr34, respectively. Lr46 and Lr34 are race nonspecific adult plant resistance (APR) genes for leaf rust and stripe rust and powdery mildew. QLr.hebau-4BL showed multiple disease resistance to leaf rust, stripe rust, Fusarium head blight, and powdery mildew. The QTL identified in this study, as well as their closely linked markers, may potentially be used in marker-assisted selection in wheat breeding.
Collapse
Affiliation(s)
- Pu Gao
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, Hebei, China
| | - Yue Zhou
- Baoding University, Baoding 071001, Hebei, China
| | | | - Peipei Zhang
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, Hebei, China
| | - Siman Wang
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, Hebei, China
| | - Daqun Liu
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, Hebei, China
| | - Zaifeng Li
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, Hebei, China
| |
Collapse
|
6
|
Velasco VV, Ochiai T, Tsudzuki M, Goto N, Ishikawa A. Quantitative trait loci mapping of innate fear behavior in day-old F2 chickens of Japanese Oh-Shamo and White Leghorn breeds using restriction site-associated DNA sequencing. Poult Sci 2024; 103:103228. [PMID: 37989001 PMCID: PMC10667749 DOI: 10.1016/j.psj.2023.103228] [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] [Received: 09/13/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 11/23/2023] Open
Abstract
Understanding the genetic mechanisms that underlie innate fear behavior is essential for improving the management and performance of the poultry industry. This study aimed to map QTL associated with innate fear responses in open field (OF) and tonic immobility (TI) tests, using an F2 chicken intercross population between 2 behaviorally distinct breeds: the aggressive Japanese Oh-Shamo (OSM) and the docile White Leghorn T-line (WL-T). Genome-wide QTL analysis for the OF and TI traits was conducted using 2,109 single nucleotide polymorphism (SNP) markers obtained through restriction site-associated DNA sequencing (RAD-seq). While several suggestive QTL were identified for TI and OF traits at genome-wide 20% significance threshold levels, the analysis revealed 2 significant QTL for 2 OF traits (total distance and maximum speed) at genome-wide 5% significance threshold levels. These significant QTL were located between 12.34 and 30.49 megabase (Mb) on chromosome 1 and between 40.02 and 63.38 Mb on chromosome 2, explaining 6.75 to 7.40% of the total variances. These findings provide valuable insights for the poultry industry, particularly in refining chicken management strategies and informing targeted breeding efforts.
Collapse
Affiliation(s)
| | - Takayuki Ochiai
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Masaoki Tsudzuki
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8528, Japan
| | - Naoki Goto
- Hendrix Genetics BU Layers, Boxmeer 5831 CK, The Netherlands
| | - Akira Ishikawa
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.
| |
Collapse
|
7
|
Qiu L, Su J, Fu Y, Zhang K. Genetic and Transcriptome Analyses of Callus Browning in Chaling Common Wild Rice ( Oryza rufipogon Griff.). Genes (Basel) 2023; 14:2138. [PMID: 38136960 PMCID: PMC10742633 DOI: 10.3390/genes14122138] [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: 10/19/2023] [Revised: 11/15/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
Callus browning during tissue culture of indica rice is genotype dependent, thus limiting the application of genetic transformation for editing-assisted breeding and elucidation of gene function. Here, using 124 introgression lines (HCLs) derived from a cross between the indica rice 9311 and Chaling common wild rice and 2059 SNPs for single-point and interval analysis, we identified two major QTLs, qCBT7 on chromosome 7 and qCBT10 on chromosome 10, related to callus browning, explaining 8-13% of callus browning. Moreover, we performed RNA-seq of two introgression lines with low callus browning, HCL183 and HCL232, with Oryza. rufipogon introgression fragments on chromosomes 10 and 7, respectively. Three candidate genes (Os07g0620700, Os10g0361000, and Os10g0456800) with upregulation were identified by combining interval mapping and weighted gene coexpression network analysis using the DEGs. The qRT-PCR results of the three candidate genes were consistent with those of RNA-seq. The differentiation of indica and japonica subspecies Oryza. sativa and Oryza. rufipogon suggests that these candidate genes are possibly unique in Oryza. rufipogon. GO analyses of hub genes revealed that callus browning may be mainly associated with ethylene and hormone signaling pathways. The results lay a foundation for future cloning of qCBT7 or qCBT10 and will improve genetic transformation efficiency in rice.
Collapse
Affiliation(s)
| | | | | | - Kun Zhang
- National Center for Evaluation of Agricultural Wild Plants (Rice), Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China; (L.Q.); (J.S.); (Y.F.)
| |
Collapse
|
8
|
Chhetri M, Miah H, Wong D, Hayden M, Bansal U, Bariana H. Mapping of a Stripe Rust Resistance Gene Yr72 in the Common Wheat Landraces AUS27506 and AUS27894 from the Watkins Collection. Genes (Basel) 2023; 14:1993. [PMID: 38002936 PMCID: PMC10671306 DOI: 10.3390/genes14111993] [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] [Received: 10/03/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 11/26/2023] Open
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is among the major threats to global wheat production. The common wheat landraces AUS27506 and AUS27894 displayed stripe rust resistance against several commercially prevailing Pst pathotypes. These genotypes were crossed with a stripe-rust-susceptible landrace AUS27229 to understand the inheritance of resistance and to determine the genomic location(s) of underlying gene(s). F3 generations of crosses AUS27506/AUS27229 and AUS27894/AUS27229 showed monogenic segregation for stripe rust resistance under greenhouse conditions. The absence of segregation for stripe rust response among the AUS27506/AUS27894-derived F3 population suggested that both genotypes carry the same gene. The stripe rust resistance gene carried by AUS27506 and AUS27894 was tentatively named YrAW4. A bulked segregant analysis placed YrAW4 in the long arm of chromosome 2B. The AUS27506/AUS27229 F3 population was enhanced to develop an F6 recombinant inbred line (RIL) population for detailed mapping of chromosome 2BL. DArT-based SSR, STS and SNP markers were employed to enrich the 2BL map. DArT-based STS markers sun481 and SNP marker IWB12294 flanked YrAW4 proximally (1.8 cM) and distally (1.2 cM), respectively. Deletion mapping placed sun481 in the deletion bin 2BL-5. All stripe rust resistance genes, previously located on chromosome 2BL, neither express an infection type like YrAW4, nor are they mapped in the deletion bin 2BL-5. Hence, YrAW4 represented a new locus and was formally named Yr72. The usefulness of the markers IWB12294 and sun481 in marker-assisted selection was demonstrated by the amplification of alleles that are different to that linked with Yr72 in 19 common wheat and two durum wheat cultivars.
Collapse
Affiliation(s)
- Mumta Chhetri
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, 107 Cobbitty Road, Cobbitty, NSW 2570, Australia; (M.C.); (H.M.)
| | - Hanif Miah
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, 107 Cobbitty Road, Cobbitty, NSW 2570, Australia; (M.C.); (H.M.)
| | - Debbie Wong
- AgriBioCentre, Department of Environment and Primary Industries, La Trobe Research and Development Park, Bundoora, VIC 3082, Australia; (D.W.); (M.H.)
| | - Matthew Hayden
- AgriBioCentre, Department of Environment and Primary Industries, La Trobe Research and Development Park, Bundoora, VIC 3082, Australia; (D.W.); (M.H.)
| | - Urmil Bansal
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, 107 Cobbitty Road, Cobbitty, NSW 2570, Australia; (M.C.); (H.M.)
| | - Harbans Bariana
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, 107 Cobbitty Road, Cobbitty, NSW 2570, Australia; (M.C.); (H.M.)
- School of Science, Western Sydney University, Bourke Road, Richmond, NSW 2753, Australia
| |
Collapse
|
9
|
Dahanayaka BA, Martin A. Multi-parental fungal mapping population study to detect genomic regions associated with Pyrenophora teres f. teres virulence. Sci Rep 2023; 13:9804. [PMID: 37328500 PMCID: PMC10275933 DOI: 10.1038/s41598-023-36963-y] [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] [Received: 03/08/2023] [Accepted: 06/13/2023] [Indexed: 06/18/2023] Open
Abstract
In recent years multi-parental mapping populations (MPPs) have been widely adopted in many crops to detect quantitative trait loci (QTLs) as this method can compensate for the limitations of QTL analyses using bi-parental mapping populations. Here we report the first multi-parental nested association mapping (MP-NAM) population study used to detect genomic regions associated with host-pathogenic interactions. MP-NAM QTL analyses were conducted on 399 Pyrenophora teres f. teres individuals using biallelic, cross-specific and parental QTL effect models. A bi-parental QTL mapping study was also conducted to compare the power of QTL detection between bi-parental and MP-NAM populations. Using MP-NAM with 399 individuals detected a maximum of eight QTLs with a single QTL effect model whilst only a maximum of five QTLs were detected with an individual bi-parental mapping population of 100 individuals. When reducing the number of isolates in the MP-NAM to 200 individuals the number of QTLs detected remained the same for the MP-NAM population. This study confirms that MPPs such as MP-NAM populations can be successfully used in detecting QTLs in haploid fungal pathogens and that the power of QTL detection with MPPs is greater than with bi-parental mapping populations.
Collapse
Affiliation(s)
- Buddhika A Dahanayaka
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4350, Australia
| | - Anke Martin
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4350, Australia.
| |
Collapse
|
10
|
Li Y, Wu S, Huang Y, Ma X, Tan L, Liu F, Lv Q, Zhu Z, Hu M, Fu Y, Zhang K, Gu P, Xie D, Sun H, Sun C. OsMADS17 simultaneously increases grain number and grain weight in rice. Nat Commun 2023; 14:3098. [PMID: 37248234 DOI: 10.1038/s41467-023-38726-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 05/11/2023] [Indexed: 05/31/2023] Open
Abstract
During the processes of rice domestication and improvement, a trade-off effect between grain number and grain weight was a major obstacle for increasing yield. Here, we identify a critical gene COG1, encoding the transcription factor OsMADS17, with a 65-bp deletion in the 5' untranslated region (5' UTR) presented in cultivated rice increasing grain number and grain weight simultaneously through decreasing mRNA translation efficiency. OsMADS17 controls grain yield by regulating multiple genes and that the interaction with one of them, OsAP2-39, has been characterized. Besides, the expression of OsMADS17 is regulated by OsMADS1 directly. It indicates that OsMADS1-OsMADS17-OsAP2-39 participates in the regulatory network controlling grain yield, and downregulation of OsMADS17 or OsAP2-39 expression can further improve grain yield by simultaneously increasing grain number and grain weight. Our findings provide insights into understanding the molecular basis co-regulating rice yield-related traits, and offer a strategy for breeding higher-yielding rice varieties.
Collapse
Affiliation(s)
- Yuanjie Li
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
- MOE Key Laboratory of Bioinformatics, Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing, 100084, China
| | - Sheng Wu
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
- MOE Key Laboratory of Bioinformatics, Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing, 100084, China
| | - Yongyu Huang
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Xin Ma
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Lubin Tan
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Fengxia Liu
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Qiming Lv
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Zuofeng Zhu
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Meixia Hu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Yongcai Fu
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Kun Zhang
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Ping Gu
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Daoxin Xie
- MOE Key Laboratory of Bioinformatics, Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing, 100084, China
| | - Hongying Sun
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China.
| | - Chuanqing Sun
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China.
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
| |
Collapse
|
11
|
Sahoo J, Mahanty B, Mishra R, Joshi RK. Development of SNP markers linked to purple blotch resistance for marker-assisted selection in onion ( Allium cepa L.) breeding. 3 Biotech 2023; 13:137. [PMID: 37124987 PMCID: PMC10130247 DOI: 10.1007/s13205-023-03562-7] [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: 06/22/2022] [Accepted: 04/15/2023] [Indexed: 05/02/2023] Open
Abstract
Purple blotch (PB), caused by Alternaria porri (Ellis) Cifferi, is one of the most destructive diseases of onion worldwide. Rapid development and deployment of resistant onion varieties is the most effective approach to control this disease. A single dominant gene, ApR1 was previously linked to PB resistance in onion cultivar 'Arka Kalyan'. In this study, an advanced RIL population derived from a cross between the resistant (Arka Kalyan) and susceptible (Agrifound Rose) cultivar of onion was used to fine map the resistant locus with SNP markers. Twenty plants from the RIL population, ten each with disease resistance and susceptibility trait, were subjected to restriction site-associated DNA sequencing (RAD-Seq) and generated 7388 single nucleotide polymorphisms (SNPs). Correlation analysis between marker genotypes and PB disease phenotype on the 20 plants identified 27 SNPs as candidate markers linked to ApR1 gene for PB resistance. Six candidate SNPs were converted to Kompetitive Allele-Specific PCR (KASP) markers designated as ApRsnip5, ApRsnip8, ApRsnip14, ApRsnip21, ApRsnip23 and ApRsnip25. Marker-trait association based on disease phenotyping and KASP genotyping data on 153 RILs confirmed that all six KASP markers were tightly associated with ApR1 gene within the genetic distance of 1.3 CentiMorgan (cM). ApRsnip14 co-segregated with the ApR1 locus. Further, the six KASP markers were tested on 27 onion lines with different genetic backgrounds. ApRsnip14, ApRsnip21, ApRsnip5 and ApRsnip23 not only showed the correct resistance allele in 3 resistance genotypes, but also clustered together in the remaining 24 susceptible lines. Alternatively, ApRsnip8 and ApRsnip25 exhibited false positives in two onion lines which do not have the R-gene. Overall, our results suggest that ApRsnip14 and ApRsnip23 with their close linkage to ApR1 locus and greater applicability on breeding germplasm are recommended in marker-assisted selection for PB resistance in onion breeding program. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03562-7.
Collapse
Affiliation(s)
- Jayashree Sahoo
- Department of Biotechnology, Rama Devi Women’s University, Vidya Vihar, Bhubaneswar, Odisha 751022 India
| | - Bijayalaxmi Mahanty
- Department of Biotechnology, Rama Devi Women’s University, Vidya Vihar, Bhubaneswar, Odisha 751022 India
| | - Rukmini Mishra
- School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha India
| | - Raj Kumar Joshi
- Department of Biotechnology, Rama Devi Women’s University, Vidya Vihar, Bhubaneswar, Odisha 751022 India
| |
Collapse
|
12
|
Mapping quantitative trait loci associated with callus browning in Dongxiang common wild rice (Oryza rufipogon Griff.). Mol Biol Rep 2023; 50:3129-3140. [PMID: 36692673 DOI: 10.1007/s11033-023-08279-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 01/12/2023] [Indexed: 01/25/2023]
Abstract
BACKGROUND Genetic transformation of indica rice (Oryza sativa ssp. indica) is limited by callus browning, which results in poor in vitro tissue culturability. Elucidating the genes in common wild rice (Oryza rufipogon Griff.) that control callus browning is fundamental for improving the tissue culturability of indica rice varieties. METHODS AND RESULTS We used a population of 129 O. rufipogon (Dongxiang common wild rice; DXCWR) introgression lines in the elite cultivar GC2 (Oryza sativa ssp. indica) background and 159 simple sequence repeat (SSR) markers to identify quantitative trait loci (QTLs) associated with callus browning. We evaluated callus browning based on the indices of callus browning rate (CBR), callus browning index (CBI), and standard callus browning index (SCBI). CONCLUSIONS We detected 30 QTLs associated with callus browning across all lines, mapping to chromosomes 1, 2, 3, 4, 8, 9, and 12. These genomic regions were repeatedly associated with differences in CBR, CBI, and SCBI. The alleles from DXCWR showed additive effects in reducing callus browning. We identified new QTLs near the markers RM247 and RM7003 on chromosome 12, indicating that these QTLs are unique to DXCWR. Furthermore, we identified six introgression lines with significantly lower callus browning. These lines will be useful germplasms for genetic transformation and fine-mapping of the culturability trait.
Collapse
|
13
|
Dhariwal R, Hiebert CW, Randhawa HS. QTL analysis identified two major all-internodes solidness loci from a completely solid-stemmed spring wheat line. FRONTIERS IN PLANT SCIENCE 2022; 13:1035620. [PMID: 36457538 PMCID: PMC9707402 DOI: 10.3389/fpls.2022.1035620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 09/27/2022] [Indexed: 06/17/2023]
Abstract
The culms of solid-stemmed wheat cultivars are filled with "pith" - a parenchymatous tissue largely composed of soft, spongy, and compact parenchyma cells. Breeding solid-stemmed cultivars is the most effective way to decrease the detrimental impact of wheat stem sawfly (WSS), Cephus cinctus Norton (Hymenoptera: Cephidae) on wheat production. Although a major solid stem gene has been previously identified from durum wheat, it produces an intermediate level of stem solidness in common wheat which is insufficient to provide the required level of WSS resistance. The maximum resistance is achieved when stems are totally filled with pith. Thus, to identify a secondary source of solidness in common wheat, we developed three mapping populations from wheat cvs. Sadash, 'AAC Innova' and 'AAC Cameron', each crossed separately with P2711, a completely solid-stemmed hexaploid wheat breeding line. All populations were genotyped using either wheat 15K or 90K Infinium iSelect SNP Assay and high-density linkage maps were generated from individual populations along with consensus maps for chromosomes 3B and 3D from all populations. 'Sadash/P2711' and 'AAC Innova/P2711' populations were subjected to extensive phenotyping in ≥3 environments followed by quantitative trait loci (QTL) analyses using population-specific and consensus linkage maps. We identified two major solid stem QTLs in the distal regions of chromosome arms 3BL and 3DL in both populations in addition to several population-specific or common minor QTLs. Internode-specific QTL analyses detected both major QTLs of chromosomes 3B and 3D across internodes, from top to bottom of the stalk, but minor QTLs were largely detected in upper or middle internodes. Our results suggest that both major QTLs are sufficient to develop highly solid-stemmed cvs; however, the minor loci, which additively enhance the pith expression, can be coupled with major genes to achieve a complete solid stem phenotype in common wheat. Comparative and haplotype analyses showed that the 3B locus is homoeologous to 3D, the former being mapped to a 1.1 Mb genomic region. Major QTLs identified in this study can be incorporated in modern wheat cultivars to achieve maximum WSS resistance from high pith expression.
Collapse
Affiliation(s)
- Raman Dhariwal
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
| | - Colin W. Hiebert
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, Morden, MB, Canada
| | - Harpinder S. Randhawa
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
| |
Collapse
|
14
|
Plewiński P, Rychel-Bielska S, Kozak B, Maureira-Butler IJ, Iqbal MM, Nelson MN, Książkiewicz M. FLOWERING LOCUS T indel variants confer vernalization-independent and photoperiod-insensitive flowering of yellow lupin ( Lupinus luteus L.). HORTICULTURE RESEARCH 2022; 9:uhac180. [PMID: 36338848 PMCID: PMC9627521 DOI: 10.1093/hr/uhac180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/04/2022] [Indexed: 06/16/2023]
Abstract
Ongoing climate change has considerably reduced the seasonal window for crop vernalization, concurrently expanding cultivation area into northern latitudes with long-day photoperiod. To address these changes, cool season legume breeders need to understand molecular control of vernalization and photoperiod. A key floral transition gene integrating signals from these pathways is the Flowering locus T (FT). Here, a recently domesticated grain legume, yellow lupin (Lupinus luteus L.), was explored for potential involvement of FT homologues in abolition of vernalization and photoperiod requirements. Two FTa (LlutFTa1a and LlutFTa1b) and FTc (LlutFTc1 and LlutFTc2) homologues were identified and sequenced for two contrasting parents of a reference recombinant inbred line (RIL) population, an early-flowering cultivar Wodjil and a late-flowering wild-type P28213. Large deletions were detected in the 5' promoter regions of three FT homologues. Quantitative trait loci were identified for flowering time and vernalization response in the RIL population and in a diverse panel of wild and domesticated accessions. A 2227 bp deletion found in the LlutFTc1 promoter was linked with early phenology and vernalization independence, whereas LlutFTa1a and LlutFTc2 indels with photoperiod responsiveness. Comparative mapping highlighted convergence of FTc1 indel evolution in two Old World lupin species, addressing both artificial selection during domestication and natural adaptation to short season environmental conditions. We concluded that rapid flowering in yellow lupin is associated with the de-repression of the LlutFTc1 homologue from the juvenile phase, putatively due to the elimination of all binding sites in the promoter region for the AGAMOUS-like 15 transcription factor.
Collapse
Affiliation(s)
- Piotr Plewiński
- Department of Gene Structure and Function, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Sandra Rychel-Bielska
- Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - Bartosz Kozak
- Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - Iván J Maureira-Butler
- Instituto de Producción y Sanidad Vegetal, Facultad de Ciencias Agrarias y Alimentarias, Universidad Austral de Chile, Valdivia, Chile
| | - Muhammad Munir Iqbal
- Centre for Plant Genetics and Breeding, The University of Western Australia, Perth, 6009, WA, Australia
- Genomics WA, Joint initiative of Telethon Kids Institute, Harry Perkins Institute of Medical Research and The University of Western Australia, QEII campus, Nedlands, 6009, Western Australia, Australia
| | - Matthew N Nelson
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Australia
| | | |
Collapse
|
15
|
Aslam K, Naveed SA, Sabar M, Shabir G, Shah SM, Khan AR, Shah MM, Fiaz S, Xu J, Arif M. Identification of QTLs for rice grain size and weight by high-throughput SNP markers in the IR64 x Sadri population. Front Genet 2022; 13:955347. [PMID: 36061203 PMCID: PMC9437704 DOI: 10.3389/fgene.2022.955347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 06/29/2022] [Indexed: 11/13/2022] Open
Abstract
Grain appearance is one of the most important attributes of rice. It is determined by grain size, shape, and weight, which in turn influences the rice yield and market value. In this study, QTLs for grain length, grain width, grain length/width ratio, and grain weight were mapped using the high-throughput indica/indica SNP platforms. The population of the mega indica variety IR64 and the high-quality aromatic variety Sadri from Iran was phenotyped. Based on this phenotypic data, plants of 94 F2:3 families including both parents were selected. A linkage map analysis of 210 SNP markers identified 14 QTLs controlling the grain length, grain width, length/width ratio, and 1,000 grain weight. Among these 14, one important region containing the QTLs for all the four studies’ traits was mapped on chromosome 8. It was derived from Sadri for the decreased length/width ratio and increased grain weight. This study demonstrated the speed and efficiency in using multiplex SNP genotyping for QTL analysis. Moreover, this study identified four novel QTLs (qGL8, qTGW8, qLWR8, and qGW8) sharing the same position on chromosome 8 which were linked with grain quality characteristics between one indica and one aromatic variety. It will enable more precise marker-assisted selection for grain weight, shape, and size. Further in-depth studies are required to dissect this region of interest and identify the related gene(s).
Collapse
Affiliation(s)
- Kashif Aslam
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Institute of Molecular Biology and Biotechnology, BZ University, Multan, Pakistan
- *Correspondence: Kashif Aslam, ; Jianlong Xu,
| | - Shahzad Amir Naveed
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- National Institute for Genomics and Advanced Biotechnology (NIGAB), Islamabad, Pakistan
| | | | - Ghulam Shabir
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Shahid Masood Shah
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad, Pakistan
| | - Abdul Rehman Khan
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad, Pakistan
| | - Muhammad Musaddiq Shah
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Jianlong Xu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Kashif Aslam, ; Jianlong Xu,
| | - Muhammad Arif
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| |
Collapse
|
16
|
Yang F, Zhang J, Zhao Y, Liu Q, Islam S, Yang W, Ma W. Wheat glutamine synthetase TaGSr-4B is a candidate gene for a QTL of thousand grain weight on chromosome 4B. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2369-2384. [PMID: 35588016 PMCID: PMC9271121 DOI: 10.1007/s00122-022-04118-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/25/2022] [Indexed: 06/14/2023]
Abstract
Glutamine synthetase TaGSr-4B is a candidate gene for a QTL of thousand grain weight on 4B, and the gene marker is ready for wheat breeding. A QTL for thousand grain weight (TGW) in wheat was previously mapped on chromosome 4B in a DH population of Westonia × Kauz. For identifying the candidate genes of the QTL, wheat 90 K SNP array was used to saturate the existing linkage map, and four field trials plus one glasshouse experiment over five locations were conducted to refine the QTL. Three nitrogen levels were applied to two of those field trials, resulting in a TGW phenotype data set from nine environments. A robust TGW QTL cluster including 773 genes was detected in six environments with the highest LOD value of 13.4. Based on differentiate gene expression within the QTL cluster in an RNAseq data of Westonia and Kauz during grain filling, a glutamine synthesis gene (GS: TaGSr-4B) was selected as a potential candidate gene for the QTL. A SNP on the promoter region between Westonia and Kauz was used to develop a cleaved amplified polymorphic marker for TaGSr-4B gene mapping and QTL reanalysing. As results, TGW QTL appeared in seven environments, and in four out of seven environments, the TGW QTL were localized on the TaGSr-4B locus and showed significant contributions to the phenotype. Based on the marker, two allele groups of Westonia and Kauz formed showed significant differences on TGW in eight environments. In agreement with the roles of GS genes on nitrogen and carbon remobilizations, TaGSr-4B is likely the candidate gene of the TGW QTL on 4B and the TaGSr-4B gene marker is ready for wheat breeding.
Collapse
Affiliation(s)
- Fan Yang
- Australian-China Joint Centre for Wheat Improvement, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, 4 Shizishan Road, Chengdu, 610066, China
| | - Jingjuan Zhang
- Australian-China Joint Centre for Wheat Improvement, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia.
| | - Yun Zhao
- Australian-China Joint Centre for Wheat Improvement, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
- College of Agronomy, Qingdao Agriculture University, Qingdao, 266109, China
| | - Qier Liu
- Australian-China Joint Centre for Wheat Improvement, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Shahidul Islam
- Australian-China Joint Centre for Wheat Improvement, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Wuyun Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, 4 Shizishan Road, Chengdu, 610066, China
| | - Wujun Ma
- Australian-China Joint Centre for Wheat Improvement, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia.
- College of Agronomy, Qingdao Agriculture University, Qingdao, 266109, China.
| |
Collapse
|
17
|
Nakano T, Takenaka M, Sugiyama M, Ishikawa A. QTL Mapping for Age-Related Eye Pigmentation in the Pink-Eyed Dilution Castaneus Mutant Mouse. Genes (Basel) 2022; 13:genes13071138. [PMID: 35885921 PMCID: PMC9318509 DOI: 10.3390/genes13071138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/17/2022] [Accepted: 06/22/2022] [Indexed: 11/16/2022] Open
Abstract
Pink-eyed dilution castaneus (Oca2p-cas) is a mutant gene on mouse chromosome 7 that arose spontaneously in wild Mus musculus castaneus. Homozygotes for Oca2p-cas exhibit pink eyes and a light gray coat throughout life. In an ordinary mutant strain carrying Oca2p-cas, we previously discovered a novel spontaneous mutation that gradually increases melanin pigmentation in the eyes and coat with aging, and we developed a novel mutant strain that was fixed for the novel phenotype. The purpose of this study was to map major quantitative trait loci (QTLs) for the novel pigmentation phenotype and for expression levels of four important melanogenesis genes, microphthalmia-associated transcription factor (Mitf), tyrosinase (Tyr), tyrosinase-related protein-1 (Tyrp1) and dopachrome tautomerase (Dct). We developed 69 DNA markers and created 303 F2 mice from two reciprocal crosses between novel and ordinary mutant strains. The QTL analysis using a selective genotyping strategy revealed a significant QTL for eye pigmentation between 34 and 64 Mb on chromosome 13. This QTL explained approximately 20% of the phenotypic variance. The QTL allele derived from the novel strain increased pigmentation. Although eye pigmentation was positively correlated with Dct expression, no expression QTLs were found, suggesting that the pigmentation QTL on chromosome 13 may not be directly in the pathway of any of the four melanogenesis genes. This study is the first step toward identifying a causal gene for the novel spontaneous phenotype in mice and is expected to discover a new regulatory mechanism for complex melanin biosynthesis during aging.
Collapse
Affiliation(s)
- Takaya Nakano
- Laboratory of Animal Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan; (T.N.); (M.T.)
| | - Momoko Takenaka
- Laboratory of Animal Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan; (T.N.); (M.T.)
| | - Makoto Sugiyama
- Faculty of Veterinary Medicine, Kitasato University School of Veterinary Medicine, Towada 034-8628, Japan;
| | - Akira Ishikawa
- Laboratory of Animal Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan; (T.N.); (M.T.)
- Correspondence:
| |
Collapse
|
18
|
Dahanayaka BA, Snyman L, Vaghefi N, Martin A. Using a Hybrid Mapping Population to Identify Genomic Regions of Pyrenophora teres Associated With Virulence. FRONTIERS IN PLANT SCIENCE 2022; 13:925107. [PMID: 35812984 PMCID: PMC9260246 DOI: 10.3389/fpls.2022.925107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 05/27/2022] [Indexed: 05/26/2023]
Abstract
Net blotches caused by Pyrenophora teres are important foliar fungal diseases of barley and result in significant yield losses of up to 40%. The two types of net blotch, net-form net blotch and spot-form net blotch, are caused by P. teres f. teres (Ptt) and P. teres f. maculata (Ptm), respectively. This study is the first to use a cross between Ptt and Ptm to identify quantitative trait loci (QTL) associated with virulence and leaf symptoms. A genetic map consisting of 1,965 Diversity Arrays Technology (DArT) markers was constructed using 351 progenies of the Ptt/Ptm cross. Eight barley cultivars showing differential reactions to the parental isolates were used to phenotype the hybrid progeny isolates. Five QTL associated with virulence and four QTL associated with leaf symptoms were identified across five linkage groups. Phenotypic variation explained by these QTL ranged from 6 to 16%. Further phenotyping of selected progeny isolates on 12 more barley cultivars revealed that three progeny isolates are moderately to highly virulent across these cultivars. The results of this study suggest that accumulation of QTL in hybrid isolates can result in enhanced virulence.
Collapse
Affiliation(s)
| | - Lislé Snyman
- Department of Agriculture and Fisheries Queensland, Hermitage Research Facility, Warwick, QLD, Australia
| | - Niloofar Vaghefi
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, Australia
- School of Agriculture and Food, University of Melbourne, Parkville, VIC, Australia
| | - Anke Martin
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, Australia
| |
Collapse
|
19
|
Mago R, Chen C, Xia X, Whan A, Forrest K, Basnet BR, Perera G, Chandramohan S, Randhawa M, Hayden M, Bansal U, Huerta-Espino J, Singh RP, Bariana H, Lagudah E. Adult plant stem rust resistance in durum wheat Glossy Huguenot: mapping, marker development and validation. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1541-1550. [PMID: 35199199 DOI: 10.1007/s00122-022-04052-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/28/2022] [Indexed: 05/12/2023]
Abstract
Adult plant stem rust resistance locus, QSrGH.cs-2AL, was identified in durum wheat Glossy Huguenot and mendelised as Sr63. Markers closely linked with Sr63 were developed. An F3 population from a Glossy Huguenot (GH)/Bansi cross used in a previous Australian study was advanced to F6 for molecular mapping of adult plant stem rust resistance. Maturity differences among F6 lines confounded assessments of stem rust response. GH was crossed with a stem rust susceptible F6 recombinant inbred line (RIL), GHB14 (M14), with similar maturity and an F6:7 population was developed through single seed descent method. F7 and F8 RILs were tested along with the parents at different locations. The F6 individual plants and both parents were genotyped using the 90 K single nucleotide polymorphism (SNP) wheat array. Stem rust resistance QTL on the long arms of chromosomes 1B (QSrGH.cs-1BL) and 2A (QSrGH.cs-2AL) were detected. QSrGH.cs-1BL and QSrGH.cs-2AL were both contributed by GH and explained 22% and 18% adult plant stem rust response variation, respectively, among GH/M14 RIL population. RILs carrying combinations of these QTL reduced more than 14% stem rust severity compared to those that possessed QSrGH.cs-1BL and QSrGH.cs-2AL individually. QSrGH.cs1BL was demonstrated to be the same as Sr58/Lr46/Yr29/Pm39 through marker genotyping. Lines lacking QSrGH.cs-1BL were used to Mendelise QSrGH.cs-2AL. Based on genomic locations of previously catalogued stem rust resistance genes and the QSrGH.cs-2AL map, it appeared to represent a new APR locus and was permanently named Sr63. SNP markers associated with Sr63 were converted to kompetetive allele-specific PCR (KASP) assays and were validated on a set of durum cultivars.
Collapse
Affiliation(s)
- Rohit Mago
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia.
| | - Chunhong Chen
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia
| | - Xiaodi Xia
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia
| | - Alex Whan
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia
| | - Kerrie Forrest
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, Agribio, 5 Ring Rd, Bundoora, VIC, 3083, Australia
| | - Bhoja R Basnet
- CIMMYT, Carretera Mexico-Veracruz Km 18, El Batan, Texcoco, Estado de México, Mexico
| | - Geetha Perera
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia
| | - Sutha Chandramohan
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia
| | - Mandeep Randhawa
- ICRAF House, CIMMYT Kenya, United Nations Avenue, Gigiri, Village Market, P.O. Box 1041, 00621, Nairobi, Kenya
| | - Matthew Hayden
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, Agribio, 5 Ring Rd, Bundoora, VIC, 3083, Australia
| | - Urmil Bansal
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia
| | - Julio Huerta-Espino
- Campo Experimental Valle de México, INIFAP, Chapingo, Estado de México, Mexico
| | - Ravi P Singh
- CIMMYT, Carretera Mexico-Veracruz Km 18, El Batan, Texcoco, Estado de México, Mexico
| | - Harbans Bariana
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia.
| | - Evans Lagudah
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia.
| |
Collapse
|
20
|
Yield-Related QTL Clusters and the Potential Candidate Genes in Two Wheat DH Populations. Int J Mol Sci 2021; 22:ijms222111934. [PMID: 34769361 PMCID: PMC8585063 DOI: 10.3390/ijms222111934] [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: 09/13/2021] [Revised: 10/21/2021] [Accepted: 10/28/2021] [Indexed: 11/17/2022] Open
Abstract
In the present study, four large-scale field trials using two doubled haploid wheat populations were conducted in different environments for two years. Grain protein content (GPC) and 21 other yield-related traits were investigated. A total of 227 QTL were mapped on 18 chromosomes, which formed 35 QTL clusters. The potential candidate genes underlying the QTL clusters were suggested. Furthermore, adding to the significant correlations between yield and its related traits, correlation variations were clearly shown within the QTL clusters. The QTL clusters with consistently positive correlations were suggested to be directly utilized in wheat breeding, including 1B.2, 2A.2, 2B (4.9–16.5 Mb), 2B.3, 3B (68.9–214.5 Mb), 4A.2, 4B.2, 4D, 5A.1, 5A.2, 5B.1, and 5D. The QTL clusters with negative alignments between traits may also have potential value for yield or GPC improvement in specific environments, including 1A.1, 2B.1, 1B.3, 5A.3, 5B.2 (612.1–613.6 Mb), 7A.1, 7A.2, 7B.1, and 7B.2. One GPC QTL (5B.2: 671.3–672.9 Mb) contributed by cultivar Spitfire was positively associated with nitrogen use efficiency or grain protein yield and is highly recommended for breeding use. Another GPC QTL without negatively pleiotropic effects on 2A (50.0–56.3 Mb), 2D, 4D, and 6B is suggested for quality wheat breeding.
Collapse
|
21
|
Das A, Parihar AK, Barpete S, Kumar S, Gupta S. Current Perspectives on Reducing the β-ODAP Content and Improving Potential Agronomic Traits in Grass Pea ( Lathyrus sativus L.). FRONTIERS IN PLANT SCIENCE 2021; 12:703275. [PMID: 34733297 PMCID: PMC8558212 DOI: 10.3389/fpls.2021.703275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 09/09/2021] [Indexed: 05/28/2023]
Abstract
Grass pea is well-established as one of the most resilient and versatile crops that can thrive under extreme climatic circumstances such as cold, heat, drought, salt-affected soils, submergence, and excessive rainfall along with resistance to several diseases and pests. However, despite the awareness of its virtues, its cultivation globally has decreased recently owing to the presence of a neurotoxin, β-N-oxalyl-L-α, β-diaminopropionic acid (β-ODAP), in the seedlings and seeds of this legume, which has been reported to cause neurolathyrism, a non-reversible neurological disorder in humans and animals. Significant repositories of Lathyrus germplasm are available across countries that have provided access to a wide range of agro-morphological traits as well as the low β ODAP content. Efforts have been made worldwide to use these germplasms for the genetic enhancement of grass pea to make this food safe for human consumption. Efforts on molecular breeding of this crop are also lagging. However, during the last decade, the research scenario has changed with some efforts being made toward improving this climate resilient pulse in terms of genomic resources. Molecular markers have also been used to evaluate the interspecific diversity as well as the phylogenetic relationship among the species and mapping studies. Intron-targeted amplified polymorphic, genomic simple sequence repeat, resistance genes analogs, and disease resistance markers developed for other legume species have been successfully cross-amplified in grass pea. Transcriptomic studies have recently been undertaken on grass pea by deploying several second-generation sequencing techniques. In addition, a few studies have attempted to unveil the genes and the underlying mechanism conferring biotic and abiotic stress or regulating the pathway of β-ODAP in grass pea. Proteomics has accelerated the identification studies on differential proteomes in response to salinity and low-temperature stress conditions for unveiling the common signaling pathways involved in mitigating these abiotic stresses and in discovering differentially regulated proteins. In grass pea, a metabolomics approach has been used to identify the metabolic processes associated with β-ODAP synthesis. Genome sequencing of grass pea is under way which is expected to be vital for whole-genome re-sequencing and gene annotation toward the identification of genes with novel functions. Recently, a draft genome sequence of grass pea was developed, and some efforts are underway to re-sequence a diverse panel of grass pea comprising 384 germplasm lines. Owing to the scantiness of a successful transformation protocol, research on the application of modern approaches of genome editing like the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) or CRISPR-associated protein 9 (CRISPR/Cas9) system for the engineering of signaling pathways or regulatory mechanisms seeks immediate attention to reduce the β-ODAP content in seeds and to improve the potential agronomic traits in grass pea.
Collapse
Affiliation(s)
- Arpita Das
- Bidhan Chandra Krishi Viswavidyalaya, Nadia, India
| | | | - Surendra Barpete
- Food Legumes Research Platform (FLRP), International Centre for Agricultural Research in the Dry Areas (ICARDA), Sehore, India
| | - Shiv Kumar
- International Centre for Agricultural Research in the Dry Areas (ICARDA), Rabat-Institutes, Rabat, Morocco
| | - Sanjeev Gupta
- ICAR-Indian Institute of Pulses Research, Kanpur, India
| |
Collapse
|
22
|
Baranwal DK, Bariana H, Bansal U. Genetic dissection of stripe rust resistance in a Tunisian wheat landrace Aus26670. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:54. [PMID: 37309400 PMCID: PMC10236087 DOI: 10.1007/s11032-021-01248-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/29/2021] [Indexed: 06/14/2023]
Abstract
The deployment of combinations of resistance genes in future wheat cultivars can save yield losses caused by the stripe rust pathogen (Puccinia striiformis f. sp. tritici; Pst). This relies on the availability and identification of genetically diverse sources of resistance. A Tunisian landrace Aus26670 displayed high level of stripe rust resistance against Australian Pst pathotypes. This landrace was crossed with a susceptible line Avocet 'S' (AvS) to generate 123 F7 recombinant inbred lines (RILs). The Aus26670/AvS RIL population was evaluated against three Pst pathotypes individually in greenhouse and against mixture of Pst pathotypes under field conditions for three consecutive years. Genetic analysis of the seedling stripe rust response variation data indicated the presence of an all-stage resistance (ASR) gene, and it was named YrAW12. This gene is effective against Australian Pst pathotypes 110 E143A + and 134 E16A + Yr17 + Yr27 + and is ineffective against the pathotype 239 E237A-Yr17 + Yr33 + . The RIL population was genotyped using the targeted genotyping-by-sequencing (tGBS) assay. YrAW12 was mapped in the 754.9-763.9 Mb region of the physical map of Chinese Spring and was concluded to be previously identified stripe rust resistance gene Yr72. QTL analysis suggested the involvement of four genomic regions which were named: QYr.sun-1BL/Yr29, QYr.sun-5AL, QYr.sun-5BL and QYr.sun-6DS, in controlling stripe rust resistance in Aus26670. Comparison of genomic regions detected in this study with previously reported QTL indicated the uniqueness of QYr.sun-5AL (654.5 Mb) and QYr.sun-6DS (1.4 Mb). Detailed mapping of these genomic regions will lead to permanent designation of these loci. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01248-7.
Collapse
Affiliation(s)
- Deepak Kumar Baranwal
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW 2570 Australia
- Department of Plant Breeding and Genetics, Bihar Agricultural University, Sabour, 813210 India
| | - Harbans Bariana
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW 2570 Australia
| | - Urmil Bansal
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW 2570 Australia
| |
Collapse
|
23
|
Quantitative trait loci for growth-related traits in Japanese quail (Coturnix japonica) using restriction-site associated DNA sequencing. Mol Genet Genomics 2021; 296:1147-1159. [PMID: 34251529 DOI: 10.1007/s00438-021-01806-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/16/2021] [Indexed: 10/20/2022]
Abstract
This study aimed to identify quantitative trait loci (QTLs) for growth-related traits by constructing a genetic linkage map based on single nucleotide polymorphism (SNP) markers in Japanese quail. A QTL mapping population of 277 F2 birds was obtained from an intercross between a male of a large-sized strain and three females of a normal-sized strain. Body weight (BW) was measured weekly from hatching to 16 weeks of age. Non-linear regression growth models of Weibull, Logistic, Gompertz, Richards, and Brody were analyzed, and growth curve parameters of Richards was selected as the best model to describe the quail growth curve of the F2 birds. Restriction-site associated DNA sequencing developed 125 SNP markers that were informative between their parental strains. The SNP markers were distributed on 16 linkage groups that spanned 795.9 centiMorgan (cM) with an average marker interval of 7.3 cM. QTL analysis of phenotypic traits revealed four main-effect QTLs. Detected QTLs were located on chromosomes 1 and 3 and were associated with BW from 4 to 16 weeks of age and asymptotic weight of Richards model at genome-wide significant at 1% or 5% level. No QTL was detected for BW from 0 to 3 weeks of age. This is the first report identified QTLs for asymptotic weight of the Richards parameter in Japanese quail. These results highlight that the combination of QTL studies and the RAD-seq method will aid future breeding programs identify genes underlying the QTL and the application of marker-assisted selection in the poultry industry, particularly the Japanese quail.
Collapse
|
24
|
Kanwal M, Qureshi N, Gessese M, Forrest K, Babu P, Bariana H, Bansal U. An adult plant stripe rust resistance gene maps on chromosome 7A of Australian wheat cultivar Axe. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2213-2220. [PMID: 33839800 DOI: 10.1007/s00122-021-03818-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/17/2021] [Indexed: 06/12/2023]
Abstract
An adult plant stripe rust resistance gene Yr75 was located on the long arm of chromosome 7A. Fine mapping of the region identified markers closely linked with Yr75. Australian wheat cultivar Axe produced resistant to moderately resistant stripe rust responses under field conditions and was exhibiting seedling responses varying from 33C to 3+ under greenhouse conditions. Experiments covering tests at different growth stages (2nd, 3rd and 4th leaf stages) demonstrated the clear expression of resistance at the 4th leaf stage under controlled-environment greenhouse conditions. A recombinant inbred line (RIL) population was developed from the Axe/Nyabing-3 (Nyb) cross. Genetic analysis of Axe/Nyb RIL population in the greenhouse at the 4th leaf stage showed monogenic inheritance of stripe rust resistance. Selective genotyping using the iSelect 90 K Infinium SNP genotyping array was performed, and the resistance locus was mapped to the long arm of chromosome 7A and named Yr75. The Axe/Nyb RIL population was genotyped using a targeted genotype-by-sequencing assay, and the resistance-linked SNPs were converted into kompetitive allele-specific PCR (KASP) markers. These markers were tested on the entire Axe/Nyb RIL population, and markers sunKASP_430 and sunKASP_427 showed close association with Yr75 in the Axe/Nyb RIL population. A high-resolution mapping family of 1032 F2 plants from the Axe/Nyb cross was developed and genotyped with sunKASP_430 and sunKASP_427, and these markers flanked Yr75 at 0.3 cM and 0.4 cM, respectively. These markers cover 1.24 Mb of the physical map of Chinese Spring, and this information will be useful for map-based cloning of Yr75.
Collapse
Affiliation(s)
- Mehwish Kanwal
- School of Life Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia
| | - Naeela Qureshi
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Rd, Bundoora, VIC, 3083, Australia
| | - Mesfin Gessese
- School of Life Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia
| | - Kerrie Forrest
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Rd, Bundoora, VIC, 3083, Australia
| | - Prashanth Babu
- School of Life Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia
| | - Harbans Bariana
- School of Life Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia.
| | - Urmil Bansal
- School of Life Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia.
| |
Collapse
|
25
|
Lipoxygenase in Wheat: Genetic Control and Impact on Stability of Lutein and Lutein Esters. Foods 2021; 10:foods10051149. [PMID: 34065461 PMCID: PMC8160724 DOI: 10.3390/foods10051149] [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: 04/01/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 11/17/2022] Open
Abstract
Preservation of lutein concentrations in wheat-based end-products during processing is important both for product quality and nutritional value. A key constituent involved in lutein degradation is endogenous lipoxygenase. Lutein and lutein ester concentrations were compared at intervals during storage of noodle sheets prepared from flour of wheat varieties representing a range in lipoxygenase activity, as well as in different mill streams and in different grain tissues. Higher lipoxygenase concentration was associated with an increased loss of free lutein and lutein mono-esters whereas lutein diesters appeared to be more resistant to degradation. Lutein degradation was reduced in the presence of a lipoxygenase inhibitor, when noodle sheets were heated to destroy enzyme activity or when pH was increased. In addition, three populations were used to investigate the genetic control of lipoxygenase. A previously reported mutation of Lpx-B1.1 was associated with a reduction in activity from high to intermediate whilst a new locus on chromosome 4D was associated with variation between intermediate and near-zero. The gene underlying the 4D locus is a putative lipoxygenase. Stability of lutein could be improved by deployment of the mutations at the 4B and 4D loci and/or by post-harvest storage of grain under conditions that promote esterification.
Collapse
|
26
|
Mapping of Quantitative Trait Loci Controlling Egg-Quality and -Production Traits in Japanese Quail ( Coturnix japonica) Using Restriction-Site Associated DNA Sequencing. Genes (Basel) 2021; 12:genes12050735. [PMID: 34068239 PMCID: PMC8153160 DOI: 10.3390/genes12050735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 02/07/2023] Open
Abstract
This research was conducted to identify quantitative trait loci (QTL) associated with egg-related traits by constructing a genetic linkage map based on single nucleotide polymorphism (SNP) markers using restriction-site associated DNA sequencing (RAD-seq) in Japanese quail. A total of 138 F2 females were produced by full-sib mating of F1 birds derived from an intercross between a male of the large-sized strain with three females of the normal-sized strain. Eggs were investigated at two different stages: the beginning stage of egg-laying and at 12 weeks of age (second stage). Five eggs were analyzed for egg weight, lengths of the long and short axes, egg shell strength and weight, yolk weight and diameter, albumen weight, egg equator thickness, and yolk color (L*, a*, and b* values) at each stage. Moreover, the age at first egg, the cumulative number of eggs laid, and egg production rate were recorded. RAD-seq developed 118 SNP markers and mapped them to 13 linkage groups using the Map Manager QTX b20 software. Markers were spanned on 776.1 cM with an average spacing of 7.4 cM. Nine QTL were identified on chromosomes 2, 4, 6, 10, 12, and Z using the simple interval mapping method in the R/qtl package. The QTL detected affected 10 egg traits of egg weight, lengths of the long and short axes of egg, egg shell strength, yolk diameter and weight, albumen weight, and egg shell weight at the beginning stage, yellowness of the yolk color at the second stage, and age at first egg. This is the first report to perform a quail QTL analysis of egg-related traits using RAD-seq. These results highlight the effectiveness of RAD-seq associated with targeted QTL and the application of marker-assisted selection in the poultry industry, particularly in the Japanese quail.
Collapse
|
27
|
Kumar S, Bhardwaj SC, Gangwar OP, Sharma A, Qureshi N, Kumaran VV, Khan H, Prasad P, Miah H, Singh GP, Sharma K, Verma H, Forrest KL, Trethowan RM, Bariana HS, Bansal UK. Lr80: A new and widely effective source of leaf rust resistance of wheat for enhancing diversity of resistance among modern cultivars. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:849-858. [PMID: 33388887 DOI: 10.1007/s00122-020-03735-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
A new leaf rust resistance gene Lr80 was identified and closely linked markers were developed for its successful pyramiding with other marker-tagged genes to achieve durable control of leaf rust. Common wheat landrace Hango-2, collected in 2006 from the Himalayan area of Hango, District Kinnaur, in Himachal Pradesh, exhibited a very low infection type (IT;) at the seedling stage to all Indian Puccinia triticina (Pt) pathotypes, except the pathotype 5R9-7 which produced IT 3+. Genetic analysis based on Agra Local/Hango-2-derived F3 families indicated monogenic control of leaf rust resistance, and the underlying locus was temporarily named LrH2. Bulked segregant analysis using 303 simple sequence repeat (SSR) markers located LrH2 in the short arm of chromosome 2D. An additional set of 10 chromosome 2DS-specific markers showed polymorphism between the parents and these were mapped on the entire Agra Local/Hango-2 F3 population. LrH2 was flanked by markers cau96 (distally) and barc124 (proximally). The 90 K Infinium SNP array was used to identify SNP markers linked with LrH2. Markers KASP_17425 and KASP_17148 showed association with LrH2. Comparison of seedling leaf rust response data and marker locations across different maps demonstrated the uniqueness of LrH2 and it was formally named Lr80. The Lr80-linked markers KASP_17425, KASP_17148 and barc124 amplified alleles/products different to Hango-2 in 82 Australian cultivars indicating their robustness for marker-assisted selection of this gene in wheat breeding programs.
Collapse
Affiliation(s)
- Subodh Kumar
- Indian Council of Agricultural Research (ICAR), Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India
| | - Subhash C Bhardwaj
- Indian Council of Agricultural Research (ICAR), Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India.
| | - Om P Gangwar
- Indian Council of Agricultural Research (ICAR), Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India
| | - Akanksha Sharma
- School of Life Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, Sydney, NSW, 2570, Australia
| | - Naeela Qureshi
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Rd, Bundoora, Victoria, 3083, Australia
| | - Vikas V Kumaran
- Indian Council of Agricultural Research (ICAR), Indian Agricultural Research Institute Regional Station, Wellington, Nilgiris, Tamil Nadu, 643231, India
| | - Hanif Khan
- Indian Council of Agricultural Research (ICAR), Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India
| | - Pramod Prasad
- Indian Council of Agricultural Research (ICAR), Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India
| | - Hanif Miah
- School of Life Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, Sydney, NSW, 2570, Australia
| | - Gyanendra P Singh
- Indian Council of Agricultural Research (ICAR), Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Kiran Sharma
- Indian Council of Agricultural Research (ICAR), Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India
| | - Hemlata Verma
- Indian Council of Agricultural Research (ICAR), Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India
| | - Kerrie L Forrest
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Rd, Bundoora, Victoria, 3083, Australia
| | - Richard M Trethowan
- School of Life Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, Sydney, NSW, 2570, Australia
| | - Harbans S Bariana
- School of Life Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, Sydney, NSW, 2570, Australia.
| | - Urmil K Bansal
- School of Life Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, Sydney, NSW, 2570, Australia.
| |
Collapse
|
28
|
Derkx A, Baumann U, Cheong J, Mrva K, Sharma N, Pallotta M, Mares D. A Major Locus on Wheat Chromosome 7B Associated With Late-Maturity α-Amylase Encodes a Putative ent-Copalyl Diphosphate Synthase. FRONTIERS IN PLANT SCIENCE 2021; 12:637685. [PMID: 33719315 PMCID: PMC7952997 DOI: 10.3389/fpls.2021.637685] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/28/2021] [Indexed: 05/27/2023]
Abstract
Many wheat varieties have the potential to develop unacceptably high levels of α-amylase in the grains if exposed to a cool temperature shock or simply cool temperature during the early to middle stages of grain filling. This phenomenon is referred to as late maturity α-amylase (LMA). The enzyme persists in the grain until harvest and may result in wheat with a low Falling Number that does not meet receival and export specifications. Resistance to LMA is therefore a valuable target for wheat breeders and wheat industries in general. Genetic evidence implicating a locus on the long arm of chromosome 7B in variation in LMA phenotype was confirmed in this investigation. Through intensive fine-mapping an ent-copalyl diphosphate synthase (CPS), hitherto named LMA-1, was identified as the likely candidate gene associated with variation in LMA phenotype. Single Nucleotide Polymorphisms (SNPs) within the LMA-1 coding sequence of Chinese Spring, Maringa and Halberd result in either prematurely terminated or functionally altered proteins that are associated with useful levels of resistance to LMA. LMA-1 transcripts detected in de-embryonated grain tissue from around 15 days after anthesis, several days before the synthesis of α-amylase, were low in the resistant varieties Chinese Spring and Maringa compared with LMA susceptible genotype Spica. This was associated with a dramatic reduction in the concentrations of intermediates in the gibberellin biosynthesis pathway such as GA19, evidence that LMA-1 was functioning as CPS in the gibberellin biosynthesis pathway. A survey of a large collection of Australian and international wheat varieties distinguished 9 major haplotypes at the LMA-1 locus. Generally, within classes, there was notable variation for LMA phenotype and evidence for genotypes whose resistance is presumed to be due to genetic loci located elsewhere on the wheat genome. Further investigation is required to characterize the sequence of steps between LMA-1 and α-amylase synthesis as well as to gain a better understanding of the role and potential impact of other genetic loci. Diagnostic markers for sources of resistance and SNP variation reported in this study should assist breeders to deploy resistance associated with LMA-1 variants in breeding programs.
Collapse
Affiliation(s)
- Adinda Derkx
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
| | - Ute Baumann
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
| | - Judy Cheong
- South Australian Agricultural Research Institute, Waite Precinct, Glen Osmond, SA, Australia
| | - Kolumbina Mrva
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
| | - Niharika Sharma
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
- NSW Department of Primary Industries, DPI Research and Business Excellence, Orange, NSW, Australia
| | - Margaret Pallotta
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
| | - Daryl Mares
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
| |
Collapse
|
29
|
Essa BH, Suzuki S, Nagano AJ, Elkholya SZ, Ishikawa A. QTL analysis for early growth in an intercross between native Japanese Nagoya and White Plymouth Rock chicken breeds using RAD sequencing-based SNP markers. Anim Genet 2021; 52:232-236. [PMID: 33458854 DOI: 10.1111/age.13039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/27/2020] [Indexed: 02/06/2023]
Abstract
An F2 population of 239 chickens was obtained by an intercross between Nagoya (NAG), a native Japanese breed with low growth, and White Plymouth Rock (WPR), a Western breed with high growth. Using SNP markers obtained by restriction site-associated DNA sequencing, genome-wide QTL analysis was performed and it revealed three QTL for early postnatal growth in the F2 population at genome-wide 5% significance levels. The most highly significant QTL affecting body weights at 2-4 weeks of age and weight gains at 2-3 and 0-4 weeks was located on GGA4 between 34.0 and 65.6 Mb with LOD scores of 3.9-5.9 and it explained 4.9-9.9% of the total variance of the traits. The analysis provided evidence for significant QTL on GGA2 between 105.6 and 125.2 Mb (LOD = 4.6) and on GGA1 between 51.1 and 61.6 Mb (LOD = 4.0) which had effects on body weight at 3 weeks and body weight gain at 0-1 week respectively. These two genomic regions explained 6.6 and 6.9% of the phenotypic F2 variance of the corresponding traits respectively. The allele derived from WPR at all QTL increased the corresponding traits. Neither sex-specific nor epistatic QTL was detected. The results showed that the GGA4 QTL affecting multiple traits is a key locus responsible for early growth in our chicken cross, suggesting that this QTL may make a great contribution to genetic improvement of growth performance of the NAG breed with a low growth rate.
Collapse
Affiliation(s)
- B H Essa
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan.,Department of Animal Husbandry and Animal Wealth Development, Faculty of Veterinary Medicine, Damanhour University, Damanhour, 22511, Egypt
| | - S Suzuki
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - A J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2194, Japan
| | - S Z Elkholya
- Department of Animal Husbandry and Animal Wealth Development, Faculty of Veterinary Medicine, Damanhour University, Damanhour, 22511, Egypt
| | - A Ishikawa
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| |
Collapse
|
30
|
Mares DJ, Mrva K, Cheong J, Fox R, Mather DE. Dormancy and dormancy release in white-grained wheat (Triticum aestivum L.). PLANTA 2021; 253:5. [PMID: 33387045 DOI: 10.1007/s00425-020-03518-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Dormancy in white-grained wheat is conditioned by the cumulative effects of several QTL that delay the onset of the capacity to germinate during ripening and after-ripening. Grain dormancy at harvest-ripeness is a major component of resistance to preharvest sprouting in wheat (Triticum aestivum L.) and an important trait in regions where rain is common during the harvest period. Breeding lines developed in Australia maintained their dormancy phenotype over multiple seasons and during grain ripening, the time between anthesis and the acquisition of the capacity to germinate, dormancy release, increased in line with the strength of dormancy. Genetic dissection of two dormant lines indicated that dormancy was due to the cumulative action of between one and three major genetic loci and several minor loci. This presents a significant challenge for breeders targeting environments with a high risk of sprouting where strong dormancy is desirable. Only around half of the difference in dormancy between the dormant lines and a non-dormant variety could be attributed to the major genetic loci on chromosomes 4A and 3A. A QTL that was mapped on chromosome 5A may be an orthologue of a minor QTL for dormancy in barley. At each locus, the dormancy allele increased the time to dormancy release during ripening. In combination, these alleles had cumulative effects. Embryo sensitivity to abscisic acid was related to the dormancy phenotype of the whole caryopsis, however, changes in concentrations of abscisic acid and gibberellins in embryo sections and de-embryonated grains during ripening and after-ripening could not be linked to the timing of dormancy release.
Collapse
Affiliation(s)
- Daryl J Mares
- School of Agriculture Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, Glen Osmond, SA, 5064, Australia.
| | - Kolumbina Mrva
- School of Agriculture Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, Glen Osmond, SA, 5064, Australia
| | - Judy Cheong
- SARDI, Waite Precinct, Urrbrae, SA, Australia
| | - Rebecca Fox
- School of Agriculture Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, Glen Osmond, SA, 5064, Australia
| | - Diane E Mather
- School of Agriculture Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, Glen Osmond, SA, 5064, Australia
| |
Collapse
|
31
|
Hayase Y, Amano S, Hashizume K, Tominaga T, Miyamoto H, Kanno Y, Ueno-Inoue Y, Inoue T, Yamada M, Ogata S, Balan S, Hayashi K, Miura Y, Tokudome K, Ohno Y, Nishijo T, Momiyama T, Yanagawa Y, Takizawa A, Mashimo T, Serikawa T, Sekine A, Nakagawa E, Takeshita E, Yoshikawa T, Waga C, Inoue K, Goto YI, Nabeshima Y, Ihara N, Yamakawa K, Taya S, Hoshino M. Down syndrome cell adhesion molecule like-1 (DSCAML1) links the GABA system and seizure susceptibility. Acta Neuropathol Commun 2020; 8:206. [PMID: 33256836 PMCID: PMC7706048 DOI: 10.1186/s40478-020-01082-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 11/15/2020] [Indexed: 12/18/2022] Open
Abstract
The Ihara epileptic rat (IER) is a mutant model with limbic-like seizures whose pathology and causative gene remain elusive. In this report, via linkage analysis, we identified Down syndrome cell adhesion molecule-like 1(Dscaml1) as the responsible gene for IER. A single base mutation in Dscaml1 causes abnormal splicing, leading to lack of DSCAML1. IERs have enhanced seizure susceptibility and accelerated kindling establishment. Furthermore, GABAergic neurons are severely reduced in the entorhinal cortex (ECx) of these animals. Voltage-sensitive dye imaging that directly presents the excitation status of brain slices revealed abnormally persistent excitability in IER ECx. This suggests that reduced GABAergic neurons may cause weak sustained entorhinal cortex activations, leading to natural kindling via the perforant path that could cause dentate gyrus hypertrophy and epileptogenesis. Furthermore, we identified a single nucleotide substitution in a human epilepsy that would result in one amino acid change in DSCAML1 (A2105T mutation). The mutant DSCAML1A2105T protein is not presented on the cell surface, losing its homophilic cell adhesion ability. We generated knock-in mice (Dscaml1A2105T) carrying the corresponding mutation and observed reduced GABAergic neurons in the ECx as well as spike-and-wave electrocorticogram. We conclude that DSCAML1 is required for GABAergic neuron placement in the ECx and suppression of seizure susceptibility in rodents. Our findings suggest that mutations in DSCAML1 may affect seizure susceptibility in humans.
Collapse
|
32
|
Ishikawa A, Sakaguchi M, Nagano AJ, Suzuki S. Genetic Architecture of Innate Fear Behavior in Chickens. Behav Genet 2020; 50:411-422. [PMID: 32770288 DOI: 10.1007/s10519-020-10012-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/29/2020] [Indexed: 01/12/2023]
Abstract
The genetic architecture of innate fear behavior in chickens is poorly understood. Here, we performed quantitative trait loci (QTL) analysis of innate responses to tonic immobility (TI) and open field (OF) fears in 242 newly hatched chicks of an F2 population between the native Japanese Nagoya breed and the White Leghorn breed using 881 single nucleotide polymorphism markers obtained by restriction site-associated DNA sequencing. At genome-wide 5% significance levels, four QTL for TI traits were revealed on chromosomes 1-3 and 24. Two of these loci had sex-specific effects on the traits. For OF traits, three QTL were revealed on chromosomes 2, 4 and 7. The TI and OF QTL identified showed no overlaps in genomic regions and different modes of inheritance. The three TI QTL and one OF QTL exerted antagonistic effects on the traits. The results demonstrated that context-dependent QTL underlie the variations in innate TI and OF behaviors.
Collapse
Affiliation(s)
- Akira Ishikawa
- Laboratory of Animal Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan.
| | - Marina Sakaguchi
- Laboratory of Animal Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2194, Japan
| | - Sae Suzuki
- Laboratory of Animal Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| |
Collapse
|
33
|
An Age-Related Hearing Protection Locus on Chromosome 16 of BXD Strain Mice. Neural Plast 2020; 2020:8889264. [PMID: 32587610 PMCID: PMC7298343 DOI: 10.1155/2020/8889264] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/15/2020] [Accepted: 05/21/2020] [Indexed: 12/21/2022] Open
Abstract
Inbred mouse models are widely used to study age-related hearing loss (AHL). Many genes associated with AHL have been mapped in a variety of strains. However, little is known about gene variants that have the converse function—protective genes that confer strong resistance to hearing loss. Previously, we reported that C57BL/6J (B6) and DBA/2J (D2) strains share a common hearing loss allele in Cdh23. The cadherin 23 (Cdh23) gene is a key contributor to early-onset hearing loss in humans. In this study, we tested hearing across a large family of 54 BXD strains generated from B6 to D2 crosses. Five of 54 strains maintain the normal threshold (20 dB SPL) even at 2 years old—an age at which both parental strains are essentially deaf. Further analyses revealed an age-related hearing protection (ahp) locus on chromosome 16 (Chr 16) at 57~76 Mb with a maximum LOD of 5.7. A small number of BXD strains at 2 years with good hearing correspond roughly to the percentage of humans who have good hearing at 90 years old. Further studies to define candidate genes in the ahp locus and related molecular mechanisms involved in age-related resilience or resistance to AHL are warranted.
Collapse
|
34
|
Genetic locus responsible for diabetic phenotype in the insulin hyposecretion (ihs) mouse. PLoS One 2020; 15:e0234132. [PMID: 32502168 PMCID: PMC7274380 DOI: 10.1371/journal.pone.0234132] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/19/2020] [Indexed: 12/30/2022] Open
Abstract
Diabetic animal models have made significant contributions to understanding the etiology of diabetes and to the development of new medications. Our research group recently developed a novel diabetic mouse strain, the insulin hyposecretion (ihs)mouse. The strain involves neither obesity nor insulitis but exhibits notable pancreatic β-cell dysfunction, distinguishing it from other well-characterized animal models. In ihs mice, severe impairment of insulin secretion from pancreas has been elicited by glucose or potassium chloride stimulation. To clarify the genetic basis of impaired insulin secretion, beginning with identifying the causative gene, genetic linkage analysis was performed using [(C57BL/6 × ihs) F1 × ihs] backcross progeny. Genetic linkage analysis and quantitative trait loci analysis for blood glucose after oral glucose loading indicated that a recessively acting locus responsible for impaired glucose tolerance was mapped to a 14.9-Mb region of chromosome 18 between D18Mit233 and D18Mit235 (the ihs locus). To confirm the gene responsible for the ihs locus, a congenic strain harboring the ihs locus on the C57BL/6 genetic background was developed. Phenotypic analysis of B6.ihs-(D18Mit233-D18Mit235) mice showed significant glucose tolerance impairment and markedly lower plasma insulin levels during an oral glucose tolerance test. Whole-genome sequencing and Sanger sequencing analyses on the ihs genome detected two ihs-specific variants changing amino acids within the ihs locus; both variants in Slc25a46 and Tcerg1 were predicted to disrupt the protein function. Based on information regarding gene functions involving diabetes mellitus and insulin secretion, reverse-transcription quantitative polymerase chain reaction analysis revealed that the relative abundance of Reep2 and Sil1 transcripts from ihs islets was significantly decreased whereas that of Syt4 transcripts were significantly increased compared with those of control C57BL/6 mice. Thus, Slc25a46, Tcerg1, Syt4, Reep2 and Sil1 are potential candidate genes for the ihs locus. This will be the focus of future studies in both mice and humans.
Collapse
|
35
|
Zhang N, Zhao L, Mawcha KT, Zhao C, Yang W, Liu D. Evaluation of leaf rust resistance in the Chinese wheat cultivar ‘Een1’. PeerJ 2020; 8:e8993. [PMID: 32523804 PMCID: PMC7263293 DOI: 10.7717/peerj.8993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 03/26/2020] [Indexed: 11/20/2022] Open
Abstract
Wheat cultivar Een1, 34 near isogenic lines (NILs), and two cultivars were used as plant materials to evaluate the resistance of Een1 to leaf rust disease. Infection type identification and gene postulation were carried out by inoculation of 12 Chinese Puccinia triticina (Pt) pathotypes. Based on the unique phenotype of Een1, we speculated that Een1 might carry Lr gene(s) different from the tested ones. The chromosomal locations for resistance gene to leaf rust disease was employed using SSR primers mapping the populations derived from the cross between Een1 and susceptible Thatcher. A total of 285 plants in the F2 population were tested by inoculating Pt pathotype FHNQ during the seedling stage. Results from the segregation analysis fits a ratio of 3:1 (${\chi }_{3:1}^{2}=2.37$, P = 0.12), indicating the presence of a single dominant gene in Een1 conferring resistance to FHNQ. A total of 1,255 simple sequence repeat (SSR) primers were first used to identify the likely linked markers based on bulk segregation analysis (BSA), and then those likely linked markers were further genotyped in the F2 population for linkage analysis. Our linkage analysis found that the resistance gene (LrE1) was distal to seven SSR loci on the long arm of chromosome 7B, with distances from 2.6 cM (Xgwm344) to 27.1 cM (Xgwm131). The closest marker Xgwm344 was further verified with F3 lines.
Collapse
Affiliation(s)
- Na Zhang
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, College of Plant Protection, Hebei Agricultrual University, Baoding, Hebei, China
| | - Lina Zhao
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, College of Plant Protection, Hebei Agricultrual University, Baoding, Hebei, China
| | - Kahsay Tadesse Mawcha
- Department of Plant Sciences, Aksum University Shire Campus, Shire, Tigray, Ethiopia
| | - Chenguang Zhao
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, College of Plant Protection, Hebei Agricultrual University, Baoding, Hebei, China
| | - Wenxiang Yang
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, College of Plant Protection, Hebei Agricultrual University, Baoding, Hebei, China
| | - Daqun Liu
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
36
|
Martin A, Moolhuijzen P, Tao Y, McIlroy J, Ellwood SR, Fowler RA, Platz GJ, Kilian A, Snyman L. Genomic Regions Associated with Virulence in Pyrenophora teres f. teres Identified by Genome-Wide Association Analysis and Biparental Mapping. PHYTOPATHOLOGY 2020; 110:881-891. [PMID: 31855502 DOI: 10.1094/phyto-10-19-0372-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Net form net blotch (NFNB), caused by the fungal pathogen Pyrenophora teres f. teres, is an important foliar disease present in all barley-producing regions of the world. This fungus is a hemibiotrophic and heterothallic ascomycete, where sexual recombination can lead to changes in disease expression in the host. Knowledge of the genetic architecture and genes involved in virulence is vital to increase the durability of NFNB resistance in barley cultivars. We used a genome-wide association mapping approach to characterize P. teres f. teres genomic regions associated with virulence in Australian barley cultivars. One hundred eighty-eight P. teres f. teres isolates collected across five Australian states were genotyped using Diversity Arrays Technology sequence markers and phenotyped across 20 different barley genotypes. Association mapping identified 14 different genomic regions associated with virulence, with the majority located on P. teres f. teres chromosomes 3 and 5 and one each present on chromosomes 1, 6, and 9. Four of the regions identified were confirmed by quantitative trait loci (QTL) mapping. The QTL regions are discussed in the context of their genomic architecture together with examination of their gene contents, which identified 20 predicted effectors. The number of QTL shown in this study at the population level clearly illustrates a complex genetic basis of P. teres f. teres virulence compared with pure necrotrophs, such as the wheat pathogens Parastagonospora nodorum and Parastagonospora tritici-repentis.
Collapse
Affiliation(s)
- Anke Martin
- Centre for Crop Health, University of Southern Queensland, Toowoomba, Queensland 4370, Australia
| | - Paula Moolhuijzen
- Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia 6102, Australia
| | - Yongfu Tao
- Hermitage Research Facility, Department of Agriculture & Fisheries, Warwick, Queensland 4370, Australia
| | - Judy McIlroy
- Hermitage Research Facility, Department of Agriculture & Fisheries, Warwick, Queensland 4370, Australia
| | - Simon R Ellwood
- Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia 6102, Australia
| | - Ryan A Fowler
- Hermitage Research Facility, Department of Agriculture & Fisheries, Warwick, Queensland 4370, Australia
| | - Greg J Platz
- Hermitage Research Facility, Department of Agriculture & Fisheries, Warwick, Queensland 4370, Australia
| | - Andrzej Kilian
- Diversity Arrays Technology, Bruce, Australian Capital Territory 2617, Australia
| | - Lisle Snyman
- Hermitage Research Facility, Department of Agriculture & Fisheries, Warwick, Queensland 4370, Australia
| |
Collapse
|
37
|
Rahman MS, Linsell KJ, Taylor JD, Hayden MJ, Collins NC, Oldach KH. Fine mapping of root lesion nematode (Pratylenchus thornei) resistance loci on chromosomes 6D and 2B of wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:635-652. [PMID: 31813000 DOI: 10.1007/s00122-019-03495-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 11/26/2019] [Indexed: 05/22/2023]
Abstract
Resistance QTL to root lesion nematode (Pratylenchus thornei) in wheat (Triticum aestivum), QRlnt.sk-6D and QRlnt.sk-2B, were mapped to intervals of 3.5 cM/1.77 Mbp on chromosome 6D and 1.4 cM/2.19 Mbp on chromosome 2B, respectively. Candidate resistance genes were identified in the QTL regions and molecular markers developed for marker-assisted breeding. Two previously known resistance QTL for root lesion nematode (Pratylenchus thornei) in bread wheat (Triticum aestivum), QRlnt.sk-6D and QRlnt.sk-2B, were fine-mapped using a Sokoll (moderately resistant) by Krichauff (susceptible) doubled haploid (DH) population and six newly developed recombinant inbred line populations. Bulked segregation analysis with the 90K wheat SNP array identified linked SNPs which were subsequently converted to KASP assays for mapping in the DH and RIL populations. On chromosome 6D, 60 KASP and five SSR markers spanned a total genetic distance of 23.7 cM. QRlnt.sk-6D was delimited to a 3.5 cM interval, representing 1.77 Mbp in the bread wheat cv. Chinese Spring reference genome sequence and 2.29 Mbp in the Aegilops tauschii genome sequence. These intervals contained 42 and 43 gene models in the respective annotated genome sequences. On chromosome 2B, 41 KASP and 5 SSR markers produced a map spanning 19.9 cM. QRlnt.sk-2B was delimited to 1.4 cM, corresponding 3.14 Mbp in the durum wheat cv. Svevo reference sequence and 2.19 Mbp in Chinese Spring. The interval in Chinese Spring contained 56 high-confidence gene models. Intervals for both QTL contained genes with similarity to those previously reported to be involved in disease resistance, namely genes for phenylpropanoid biosynthetic pathway-related enzymes, NBS-LRR proteins and protein kinases. The potential roles of these candidate genes in P. thornei resistance are discussed. The KASP markers reported in this study could potentially be used for marker-assisted breeding of P. thornei-resistant wheat cultivars.
Collapse
Affiliation(s)
- Muhammad Shefatur Rahman
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA, 5064, Australia
- South Australian Research and Development Institute, Glen Osmond, SA, 5064, Australia
| | - Katherine J Linsell
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA, 5064, Australia
- South Australian Research and Development Institute, Glen Osmond, SA, 5064, Australia
| | - Julian D Taylor
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Matthew J Hayden
- Department of Primary Industries, Victorian AgriBiosciences Centre, Bundoora, VIC, 3083, Australia
| | - Nicholas C Collins
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Klaus H Oldach
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA, 5064, Australia.
- South Australian Research and Development Institute, Glen Osmond, SA, 5064, Australia.
- KWS Lochow GmbH, Ferdinand-von-Lochow-Str. 5, 29303, Bergen, Germany.
| |
Collapse
|
38
|
Brown A, Schuetz D, Han Y, Daria D, Nattamai KJ, Eiwen K, Sakk V, Pospiech J, Saller T, van Zant G, Wagner W, Geiger H. The lifespan quantitative trait locus gene Securin controls hematopoietic progenitor cell function. Haematologica 2020; 105:317-324. [PMID: 31073078 PMCID: PMC7012499 DOI: 10.3324/haematol.2018.213009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 05/09/2019] [Indexed: 12/11/2022] Open
Affiliation(s)
- Andreas Brown
- Institute of Molecular Medicine and Stem Cell Aging, Ulm University, Ulm, Germany
| | - Desiree Schuetz
- Institute of Molecular Medicine and Stem Cell Aging, Ulm University, Ulm, Germany
| | - Yang Han
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Deidre Daria
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, OH, USA
| | - Kalpana J Nattamai
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, OH, USA
| | - Karina Eiwen
- Institute of Molecular Medicine and Stem Cell Aging, Ulm University, Ulm, Germany
| | - Vadim Sakk
- Institute of Molecular Medicine and Stem Cell Aging, Ulm University, Ulm, Germany
| | - Johannes Pospiech
- Institute of Molecular Medicine and Stem Cell Aging, Ulm University, Ulm, Germany
| | - Thomas Saller
- Institute of Molecular Medicine and Stem Cell Aging, Ulm University, Ulm, Germany
| | - Gary van Zant
- University of Kentucky College of Medicine, UK Medical Center, Lexington, KY, USA
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Hartmut Geiger
- Institute of Molecular Medicine and Stem Cell Aging, Ulm University, Ulm, Germany .,Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, OH, USA
| |
Collapse
|
39
|
A common wild rice-derived BOC1 allele reduces callus browning in indica rice transformation. Nat Commun 2020; 11:443. [PMID: 31974373 PMCID: PMC6978460 DOI: 10.1038/s41467-019-14265-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 12/20/2019] [Indexed: 12/22/2022] Open
Abstract
Callus browning, a common trait derived from the indica rice cultivar (Oryza sativa L.), is a challenge to transformation regeneration. Here, we report the map-based cloning of BROWNING OF CALLUS1 (BOC1) using a population derived from crossing Teqing, an elite indica subspecies exhibiting callus browning, and Yuanjiang, a common wild rice accession (Oryza rufipogon Griff.) that is less susceptible to callus browning. We show that BOC1 encodes a SIMILAR TO RADICAL-INDUCED CELL DEATH ONE (SRO) protein. Callus browning can be reduced by appropriate upregulation of BOC1, which consequently improves the genetic transformation efficiency. The presence of a Tourist-like miniature inverted-repeat transposable element (Tourist MITE) specific to wild rice in the promoter of BOC1 increases the expression of BOC1 in callus. BOC1 may decrease cell senescence and death caused by oxidative stress. Our study provides a gene target for improving tissue culturability and genetic transformation. Callus browning heavily affects indica rice transformation regeneration. Here, the authors show transposon insertion in the promoter of BOC1 gene, encoding a SIMILAR TO RADICAL-INDUCED CELL DEATH ONE protein, can upregulate its expression and decrease callus browning in cultivated rice by releasing oxidative stress.
Collapse
|
40
|
Zhang YW, Wen YJ, Dunwell JM, Zhang YM. QTL.gCIMapping.GUI v2.0: An R software for detecting small-effect and linked QTLs for quantitative traits in bi-parental segregation populations. Comput Struct Biotechnol J 2019; 18:59-65. [PMID: 31890145 PMCID: PMC6921137 DOI: 10.1016/j.csbj.2019.11.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 11/10/2019] [Accepted: 11/15/2019] [Indexed: 10/31/2022] Open
Abstract
The methodologies and software packages for mapping quantitative trait loci (QTLs) in bi-parental segregation populations are well established. However, it is still difficult to detect small-effect and linked QTLs. To address this issue, we proposed a genome-wide composite interval mapping (GCIM) in bi-parental segregation populations. To popularize this method, we developed an R package. This program with two versions (Graphical User Interface: QTL.gCIMapping.GUI v2.0 and code: QTL.gCIMapping v3.2) can be used to identify QTLs for quantitative traits in recombinant inbred lines, doubled haploid lines, backcross and F2 populations. To save running time, fread function was used to read the dataset, parallel operation was used in parameter estimation, and conditional probability calculation was implemented by C++. Once one input file with *.csv or *.txt formats is uploaded into the package, one or two output files and one figure can be obtained. The input file with the ICIM and win QTL cartographer formats is available as well. Real data analysis for 1000-grain weight in rice showed that the GCIM detects the maximum previously reported QTLs and genes, and has the minimum AIC value in the stepwise regression of all the identified QTLs for this trait; using stepwise regression and empirical Bayesian analyses, there are some false QTLs around the previously reported QTLs and genes from the CIM method. The above software packages on Windows, Mac and Linux can be downloaded from https://cran.r-project.org/web/packages/ or https://bigd.big.ac.cn/biocode/tools/7078/releases/27 in order to identify all kinds of omics QTLs.
Collapse
Affiliation(s)
- Ya-Wen Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang-Jun Wen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jim M Dunwell
- School of Agriculture, Policy and Development, University of Reading, Reading RG6 6AR, United Kingdom
| | - Yuan-Ming Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| |
Collapse
|
41
|
Mohan A, Dhaliwal AK, Nagarajan R, Gill KS. Molecular Characterization of Auxin Efflux Carrier- ABCB1 in hexaploid wheat. Sci Rep 2019; 9:17327. [PMID: 31757978 PMCID: PMC6874703 DOI: 10.1038/s41598-019-51482-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 09/29/2019] [Indexed: 11/09/2022] Open
Abstract
Auxin is an important phytohormone that regulates response, differentiation, and development of plant cell, tissue, and organs. Along with its local production, long-distance transport coordinated by the efflux/influx membrane transporters is instrumental in plant development and architecture. In the present study, we cloned and characterized a wheat (Triticum aestivum) auxin efflux carrier ABCB1. The TaABCB1 was physically localized to the proximal 15% of the short arm of wheat homoeologous group 7 chromosomes. Size of the Chinese spring (CS) homoeologs genomic copies ranged from 5.3–6.2 kb with the 7A copy being the largest due to novel insertions in its third intron. The three homoeologous copies share 95–97% sequence similarity at the nucleotide, 98–99% amino acid, and overall Q-score of 0.98 at 3-D structure level. Though detected in all analyzed tissues, TaABCB1 predominantly expressed in the meristematic tissues likely due to the presence of meristem-specific activation regulatory element identified in the promoter region. RNAi plants of TaABCB1 gene resulted in reduced plant height and increased seed width. Promoter analysis revealed several responsive elements detected in the promoter region including that for different hormones as auxin, gibberellic acid, jasmonic acid and abscisic acid, light, and circadian regulated elements.
Collapse
Affiliation(s)
- Amita Mohan
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Amandeep K Dhaliwal
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Ragupathi Nagarajan
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Kulvinder S Gill
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA.
| |
Collapse
|
42
|
Pakeerathan K, Bariana H, Qureshi N, Wong D, Hayden M, Bansal U. Identification of a new source of stripe rust resistance Yr82 in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:3169-3176. [PMID: 31463519 DOI: 10.1007/s00122-019-03416-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 08/20/2019] [Indexed: 05/13/2023]
Abstract
Stripe rust resistance gene, Yr82, was mapped in chromosome 3BL using SNP markers. Yr82 interacted with Yr29 to produce lower stripe rust responses at the adult plant stage. Landrace Aus27969 produced low infection types against Australian Puccinia striiformis f. sp. tritici (Pst) pathotypes. A recombinant inbred line (RIL) F7 population from the Aus27969/Avocet S cross was developed. Monogenic segregation for seedling stripe rust response was observed among the RIL population, and the resistance locus was named Yr82. Bulk segregant analysis performed using the iSelect wheat 90 K Infinium SNP array located Yr82 in the long arm of chromosome 3B. The RIL population was screened against stripe rust under field conditions and was genotyped with targeted genotyping-by-sequencing assay. QTL analysis detected the involvement of chromosomes 1B and 3B in controlling stripe rust resistance carried by Aus27969. Incorporation of Yr82 and marker SNPLr46G22 into the linkage map showed that the QTL in 1B and 3B represented Yr29 and Yr82, respectively. Kompetitive allele-specific PCR (KASP) markers sun KASP_300 and KASP_8775 flanked Yr82 distally and proximally, respectively, each at 2 cM distance. These Yr82-linked markers were polymorphic among 84% of Australian cultivars and can be used for marker-assisted selection of Yr82.
Collapse
Affiliation(s)
- Kandiah Pakeerathan
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia
- Department of Agricultural Biology, The University of Jaffna, Kilinochchi, Sri Lanka
| | - Harbans Bariana
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia
| | - Naeela Qureshi
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia
- Centre for AgriBioscience, Agriculture Victoria, AgriBio, 5 Ring Road, Bundoora, VIC, 3083, Australia
| | - Debbie Wong
- Centre for AgriBioscience, Agriculture Victoria, AgriBio, 5 Ring Road, Bundoora, VIC, 3083, Australia
| | - Matthew Hayden
- Centre for AgriBioscience, Agriculture Victoria, AgriBio, 5 Ring Road, Bundoora, VIC, 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Urmil Bansal
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia.
| |
Collapse
|
43
|
Rychel S, Książkiewicz M. Development of gene-based molecular markers tagging low alkaloid pauper locus in white lupin (Lupinus albus L.). J Appl Genet 2019; 60:269-281. [PMID: 31410824 PMCID: PMC6803572 DOI: 10.1007/s13353-019-00508-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/02/2019] [Accepted: 07/18/2019] [Indexed: 12/20/2022]
Abstract
White lupin (Lupinus albus L.) is a legume grain crop cultivated since ancient Greece and Egypt. Modern white lupin cultivars are appreciated as a source of protein with positive nutraceutical impact. However, white lupins produce anti-nutritional compounds, quinolizidine alkaloids, which provide bitter taste and have a negative influence on human health. During domestication of this species, several recessive alleles at unlinked loci controlling low alkaloid content were selected. One of these loci, pauper, was exploited worldwide providing numerous low-alkaloid cultivars. However, molecular tracking of pauper has been hampered due to the lack of diagnostic markers. In the present study, the synteny-based approach was harnessed to target pauper locus. Single-nucleotide polymorphisms flanking pauper locus on white lupin linkage map as well as candidate gene sequences elucidated from the narrow-leafed lupin (L. angustifolius L.) chromosome segment syntenic to the pauper linkage group region were transformed to PCR-based molecular markers. These markers were analyzed both in the mapping population and world germplasm collection. From fourteen markers screened, eleven were localized at a distance below 1.5 cM from this locus, including five co-segregating with pauper. The linkage of these markers was confirmed by high LOD values (up to 58.4). Validation performed in the set of 127 bitter and 23 sweet accessions evidenced high applicability of one marker, LAGI01_35805_F1_R1, for pauper locus selection, highlighted by the low ratio of false-positive scores (2.5%). LAGI01_35805 represents a homolog of L. angustifolius acyltransferase-like (LaAT) gene which might hypothetically participate in the alkaloid biosynthesis process in lupins.
Collapse
Affiliation(s)
- Sandra Rychel
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Michał Książkiewicz
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
| |
Collapse
|
44
|
Rahman MA, Thomson MJ, De Ocampo M, Egdane JA, Salam MA, Shah-E-Alam M, Ismail AM. Assessing trait contribution and mapping novel QTL for salinity tolerance using the Bangladeshi rice landrace Capsule. RICE (NEW YORK, N.Y.) 2019; 12:63. [PMID: 31410650 PMCID: PMC6692794 DOI: 10.1186/s12284-019-0319-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 07/25/2019] [Indexed: 05/15/2023]
Abstract
BACKGROUND Salinity is one of the most widespread abiotic stresses affecting rice productivity worldwide. The purpose of this study was to establish the relative importance of different traits associated with salinity tolerance in rice and to identify new quantitative trait loci (QTL) conferring tolerance to salinity at seedling stage. A total of 231 F2:3 plants derived from a cross between a sensitive variety BRRI dhan29 (BR29 hereafter) and Capsule, a salt tolerant Bangladeshi indica landrace, were evaluated under salt stress in a phytotron. RESULTS Out of the 231 F2 plants, 47 highly tolerant and 47 most sensitive lines were selected, representing the two extreme tails of the phenotypic distribution. These 94 plants were genotyped for 105 simple sequence repeat (SSR) and insertion/deletion (InDel) markers. A genetic linkage map spanning approximately 1442.9 cM of the 12 linkage groups with an average marker distance of 13.7 cM was constructed. QTL were identified on the long arm of chromosome 1 for Na+ concentration, K+ concentration, Na+-K+ ratio and survival; chromosome 3 for Na+ concentration, survival and overall phenotypic evaluation using the Standard Evaluation system (SES); and chromosome 5 for SES. A total of 6 pairwise epistatic interactions were also detected between QTL-linked and QTL-unlinked regions. Graphical genotyping indicated an association between the phenotypes of the extreme families and their QTL genotypes. Path coefficient analysis revealed that Na+ concentration, survival, Na+-K+ ratio and the overall phenotypic performance (SES score) are the major traits associated with salinity tolerance of Capsule. CONCLUSIONS Capsule provides an alternative source of salinity tolerance aside from Pokkali and Nona Bokra, the two Indian salt tolerant landraces traditionally used for breeding salt tolerant rice varieties. Pyramiding the new QTL identified in this study with previously discovered loci, such as Saltol, will facilitate breeding varieties that are highly tolerant of salt stress.
Collapse
Affiliation(s)
- M Akhlasur Rahman
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- Bangladesh Rice Research Institute, Gazipur, 1701, Bangladesh
| | - Michael J Thomson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Marjorie De Ocampo
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - James A Egdane
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - M A Salam
- Bangladesh Rice Research Institute, Gazipur, 1701, Bangladesh
| | - M Shah-E-Alam
- Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Abdelbagi M Ismail
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.
| |
Collapse
|
45
|
Gessese M, Bariana H, Wong D, Hayden M, Bansal U. Molecular Mapping of Stripe Rust Resistance Gene Yr81 in a Common Wheat Landrace Aus27430. PLANT DISEASE 2019; 103:1166-1171. [PMID: 30998448 DOI: 10.1094/pdis-06-18-1055-re] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The deployment of diverse sources of resistance in new cultivars underpins durable control of rust diseases. Aus27430 exhibited a moderate level of stripe rust resistance against Puccinia striiformis f. sp. tritici (Pst) pathotypes currently prevalent in Australia. Aus27430 was crossed with the susceptible parent Avocet S (AvS) and subsequent filial generations were raised. Monogenic segregation observed among Aus27430/AvS F3 families was confirmed through stripe rust screening of an F6 recombinant inbred line (RIL) population, and the resistance locus was temporarily named YrAW5. Selective genotyping using an Illumina iSelect 90K wheat SNP bead chip array located YrAW5 in chromosome 6A. Genetic mapping of the RIL population with linked 90K SNPs that were converted into PCR-based marker assays, as well as SSR markers previously mapped to chromosome 6A, confirmed the chromosomal assignment for YrAW5. Comparative analysis of other stripe rust resistance genes located in chromosome 6A led to the formal designation of YrAW5 as Yr81. Tests with a marker linked with Yr18 also demonstrated the presence of this gene in Aus27430. Yr18 interacted with Yr81 to produce stripe rust responses lower than those produced by RILs carrying these genes individually. Although gwm459 showed higher recombination with Yr81 compared with the other flanking marker KASP_3077, it amplified the AvS allele in 80 cultivars, whereas KASP_3077 amplified AvS allele in 67 cultivars. Both markers can be used in marker-assisted selection after confirming parental polymorphism.
Collapse
Affiliation(s)
- Mesfin Gessese
- 1 The University of Sydney Plant Breeding Institute, School of Life and Environment Sciences, Faculty of Science, Cobbitty, NSW 2570, Australia
| | - Harbans Bariana
- 1 The University of Sydney Plant Breeding Institute, School of Life and Environment Sciences, Faculty of Science, Cobbitty, NSW 2570, Australia
| | - Debbie Wong
- 2 Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083, Australia; and
| | - Matthew Hayden
- 2 Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083, Australia; and
- 3 School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
| | - Urmil Bansal
- 1 The University of Sydney Plant Breeding Institute, School of Life and Environment Sciences, Faculty of Science, Cobbitty, NSW 2570, Australia
| |
Collapse
|
46
|
Boonyarattanasoonthorn T, Elewa YHA, Tag-El-Din-Hassan HT, Morimatsu M, Agui T. Profiling of cellular immune responses to Mycoplasma pulmonis infection in C57BL/6 and DBA/2 mice. INFECTION GENETICS AND EVOLUTION 2019; 73:55-65. [PMID: 31026602 DOI: 10.1016/j.meegid.2019.04.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/19/2019] [Accepted: 04/21/2019] [Indexed: 11/26/2022]
Abstract
Mycoplasma infections cause respiratory tract damages and atypical pneumonia, resulting in serious problems in humans and animals worldwide. It is well known that laboratory inbred mouse strains show various susceptibility to Mycoplasma pulmonis (M. pulmonis) infection, which causes murine respiratory mycoplasmosis. In this study, we aimed to demonstrate the difference in cellular immune responses between resistant strain, C57BL/6NCrSlc (B6) and susceptible strain, DBA/2CrSlc (D2) after challenging M. pulmonis infection. D2 mice showed higher amount of bacterial proliferation in lung, higher pulmonary infiltration of immune cells such as neutrophils, macrophages, and lymphocytes, and higher levels of interleukin (IL)-1β, IL-6, IL-17A, and tumor necrosis factor-α in bronchoalveolar lavage fluid than did B6 mice. The results of this study suggest that D2 mice are more susceptible than B6 mice to M. pulmonis infection due to a hyper-immune inflammatory response.
Collapse
Affiliation(s)
- Tussapon Boonyarattanasoonthorn
- Laboratory of Laboratory Animal Science and Medicine, Department of Applied Veterinary Sciences, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Japan
| | - Yaser Hosny Ali Elewa
- Laboratory of Anatomy, Department of Basic Veterinary Sciences, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Japan; Department of Histology and Cytology, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44519, Egypt
| | - Hassan T Tag-El-Din-Hassan
- Laboratory of Laboratory Animal Science and Medicine, Department of Applied Veterinary Sciences, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Japan; Poultry Production Department, Mansoura University, Mansoura 35516, Egypt
| | - Masami Morimatsu
- Laboratory of Laboratory Animal Science and Medicine, Department of Applied Veterinary Sciences, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Japan
| | - Takashi Agui
- Laboratory of Laboratory Animal Science and Medicine, Department of Applied Veterinary Sciences, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Japan.
| |
Collapse
|
47
|
Ono T, Kouguchi T, Ishikawa A, Nagano AJ, Takenouchi A, Igawa T, Tsudzuki M. Quantitative trait loci mapping for the shear force value in breast muscle of F2 chickens. Poult Sci 2019; 98:1096-1101. [PMID: 30329107 DOI: 10.3382/ps/pey493] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 10/10/2018] [Indexed: 12/18/2022] Open
Abstract
The shear force value is one of the major traits that determine meat quality. In the present study, we performed QTL analysis for chicken breast muscle shear force value at 7 wk of age using 545 single nucleotide polymorphism (SNP) markers developed via restriction-site associated DNA sequencing (RAD-seq). An F2 resource family was generated by mating Oh-Shamo, a native Japanese chicken breed, and the White Plymouth Rock chicken breed. A total of 215 F2 birds were produced. Simple interval mapping revealed one significant main-effect QTL between 6.28 and 8.10 Mb SNPs on the chromosome Z with a logarithm of odds score of 5.53 at the genome-wide 5% level. At this QTL, the confidence interval, phenotypic variance explained, and additive effect were 26 cM, 12.24%, and -0.31 in males and -0.34 in females, respectively. No QTL with epistatic interaction effects were detected. To our knowledge, this is the first report on a QTL affecting the shear force value in the chicken breast muscle, using SNP markers derived from RAD-seq.
Collapse
Affiliation(s)
- Takashi Ono
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | | | - Akira Ishikawa
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan.,Japanese Avian Bioresource Project Research Center, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga 520-2194, Japan
| | - Atsushi Takenouchi
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Takeshi Igawa
- Japanese Avian Bioresource Project Research Center, Higashi-Hiroshima, Hiroshima 739-8528, Japan.,Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Masaoki Tsudzuki
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan.,Japanese Avian Bioresource Project Research Center, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| |
Collapse
|
48
|
Chukwu SC, Rafii MY, Ramlee SI, Ismail SI, Oladosu Y, Okporie E, Onyishi G, Utobo E, Ekwu L, Swaray S, Jalloh M. Marker-assisted selection and gene pyramiding for resistance to bacterial leaf blight disease of rice (Oryza sativa L.). BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1584054] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Samuel Chibuike Chukwu
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Selangor, Malaysia
- Department of Crop Production and Landscape Management, Faculty of Agriculture and Natural Resources Management, Ebonyi State University, Abakaliki, Nigeria
| | - Mohd Y. Rafii
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Selangor, Malaysia
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia (UPM), Selangor, Malaysia
| | - Shairul Izan Ramlee
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia (UPM), Selangor, Malaysia
| | - Siti Izera Ismail
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia (UPM), Selangor, Malaysia
| | - Yussuf Oladosu
- Department of Crop Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri, Nigeria
| | - Emmanuel Okporie
- Department of Crop Production and Landscape Management, Faculty of Agriculture and Natural Resources Management, Ebonyi State University, Abakaliki, Nigeria
| | - Godwin Onyishi
- Department of Crop Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri, Nigeria
| | - Emeka Utobo
- Department of Crop Production and Landscape Management, Faculty of Agriculture and Natural Resources Management, Ebonyi State University, Abakaliki, Nigeria
| | - Lynda Ekwu
- Department of Crop Production and Landscape Management, Faculty of Agriculture and Natural Resources Management, Ebonyi State University, Abakaliki, Nigeria
| | - Senesie Swaray
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Selangor, Malaysia
| | - Momodu Jalloh
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Selangor, Malaysia
| |
Collapse
|
49
|
Kroc M, Koczyk G, Kamel KA, Czepiel K, Fedorowicz-Strońska O, Krajewski P, Kosińska J, Podkowiński J, Wilczura P, Święcicki W. Transcriptome-derived investigation of biosynthesis of quinolizidine alkaloids in narrow-leafed lupin (Lupinus angustifolius L.) highlights candidate genes linked to iucundus locus. Sci Rep 2019; 9:2231. [PMID: 30783128 PMCID: PMC6381137 DOI: 10.1038/s41598-018-37701-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 12/12/2018] [Indexed: 01/23/2023] Open
Abstract
Unravelling the biosynthetic pathway of quinolizidine alkaloids (QAs), regarded as antinutritional compounds of narrow-leafed lupin (NLL) seeds, is fundamental to best exploit NLL as food or feed. We investigated 12 candidate genes connected to QA biosynthesis, selecting them by transcriptomic and genomic approaches, from the landscape of genes differentially expressed in leaves of the high- and low-alkaloid NLL accessions. Linkage analysis enabled the assessment of the location of the candidate genes in relation to iucundus, a major locus of unknown identity, that confers reduced QA content in seeds. The key finding was the identification of APETALA2/ethylene response transcription factor, RAP2-7, cosegregating with the iucundus locus and located within a region with highly significant QTLs that affect QA composition. We additionally identified a 4-hydroxy-tetrahydrodipicolinate synthase (DHDPS) gene involved in L-lysine biosynthesis as being closely linked to iucundus. The distributed location of other remaining candidates (including previously known QA genes) across different linkage groups, also indirectly supports the transcription factor as a possible regulator of lupin alkaloid biosynthesis. Our findings provide crucial insight into QA biosynthesis in NLL. Additionally, we evaluated and selected appropriate reference genes for qRT-PCRs to analyse the expression levels of QA genes in NLL.
Collapse
Affiliation(s)
- Magdalena Kroc
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
| | - Grzegorz Koczyk
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Katarzyna A Kamel
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Katarzyna Czepiel
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Olga Fedorowicz-Strońska
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Paweł Krajewski
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Joanna Kosińska
- Department of Medical Genetics, Medical University of Warsaw, Pawińskiego 3c, 02-106, Warsaw, Poland
| | - Jan Podkowiński
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Piotrowo 2, 61-138, Poznań, Poland
| | - Paulina Wilczura
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Wojciech Święcicki
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| |
Collapse
|
50
|
Inukai T, Nagashima S, Kato M. Pid3-I1 is a race-specific partial-resistance allele at the Pid3 blast resistance locus in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:395-404. [PMID: 30390130 DOI: 10.1007/s00122-018-3227-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 10/27/2018] [Indexed: 06/08/2023]
Abstract
The rice blast resistance QTL detected on chromosome 6 in MC276 is Pid3-I1, one of the multiple alleles at the Pid3 locus. Pid3-I1 shows race-specific partial resistance. Many of the quantitative trait loci (QTLs) for rice blast resistance reported to date remain unidentified. In the present study, we focused on qBRM6.2, a known blast-resistance QTL in experimental resistant rice line MC276. A CO39 near-isogenic line (NIL) carrying qBRM6.2 from MC276 was developed here, and we showed that qBRM6.2 resistance was partial but race specific to Japanese blast isolates using the NIL. Because defense genes in the NIL were expressed sooner than those in CO39 after inoculation with a blast isolate, qBRM6.2 resistance appeared to be an induced resistance. Next, we demonstrated that qBRM6.2 was located within a 123-kb interval on chromosome 6. Among the six genes annotated in the interval, only four genes appeared to be functional. Among these four, a polymorphism between CO39 and the NIL for qBRM6.2 at the amino acid sequence level was detected only in Os06g0330400 that encodes a fatty acid hydroxylase domain-containing protein and in Os06g0330100, the blast resistance locus Pid3, that encodes a nucleotide-binding site-leucine-rich repeat protein. Moreover, the allele at the Pid3 locus in the NIL was Pid3-I1, originally identified as a complete blast resistance gene in Kasalath. To clarify whether Pid3-I1 is qBRM6.2, we investigated the resistance phenotype of Pid3-I1 to Japanese isolates using Nipponbare transgenic lines that express Pid3-I1. The results showed that Pid3-I1 was a race-specific but partial-resistance allele at the Pid3 locus, suggesting strongly that Pid3-I1 is qBRM6.2. The discrepancy in the phenotype of Pid3-I1 between the present and previous reports is also discussed.
Collapse
Affiliation(s)
- Tsuyoshi Inukai
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan.
| | - Saki Nagashima
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Miyako Kato
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| |
Collapse
|