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Rehman F, Gong H, Ma Y, Zeng S, Ke D, Yang C, Zhao Y, Wang Y. An ultra-dense linkage map identified quantitative trait loci corresponding to fruit quality- and size-related traits in red goji berry. FRONTIERS IN PLANT SCIENCE 2024; 15:1390936. [PMID: 39297015 PMCID: PMC11408189 DOI: 10.3389/fpls.2024.1390936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 08/01/2024] [Indexed: 09/21/2024]
Abstract
Goji berries are a small-fruited shrub with industrial importance whose fruit considered beneficial in both fresh and dried forms. Current germplasms of goji berries include small fruits with a short shelf life, less sweet and bitter taste, and a lack of appropriate genetic information. This study aimed to employ whole genome resequencing to generate an ultra-dense bin linkage map and to elucidate the genetic basis of goji fruit quality and size using quantitative trait loci (QTL) mapping analysis in a cross-pollinated hybrid population. To achieve this goal, human sensory tests were carried out to determine the bitter taste (BT) and sweet taste (ST), and to quantify the soluble solid content (SSC), fruit firmness (FF), and fruit size-related traits of fresh goji fruits over three or four years. The results revealed that the goji bin linkage map based on resequencing spanned a total length of 966.42 cM and an average bin interval of 0.03 cM. Subsequent variant calling and ordering resulted in 3,058 bins containing 35,331 polymorphic markers across 12 chromosomes. A total of 99 QTLs, with individual loci in different environments explaining a phenotypic variance of 1.21-16.95% were identified for the studied traits. Ten major effects, including colocalized QTLs corresponding to different traits, were identified on chromosomes 1, 3, 5, 6, 7, and 8, with a maximum Logarithm of Odds (LOD) of 29.25 and 16.95% of explained phenotypic variance (PVE). In addition, four stable loci, one for FF, one for fruit weight (FW), and two for fruit shape index (FSI), were mainly mapped on chromosomes 5, 6, and 7, elucidating 2.10-16.95% PVE. These findings offer valuable insights into the genetic architecture of goji fruit traits along with identified specific loci and markers to further improve and develop sweeter, less bitter and larger fruited goji berry cultivars with extended shelf life.
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Affiliation(s)
- Fazal Rehman
- State Key Laboratory of Plant Diversity and Specialty Crops, Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, South China National Botanical Garden, Guangzhou, China
| | - Haiguang Gong
- State Key Laboratory of Plant Diversity and Specialty Crops, Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, South China National Botanical Garden, Guangzhou, China
| | - Yun Ma
- State Key Laboratory of Plant Diversity and Specialty Crops, Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, South China National Botanical Garden, Guangzhou, China
| | - Shaohua Zeng
- State Key Laboratory of Plant Diversity and Specialty Crops, Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, South China National Botanical Garden, Guangzhou, China
- College of Life Science, Gannan Normal University, Ganzhou, Jiangxi, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Danmin Ke
- State Key Laboratory of Plant Diversity and Specialty Crops, Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, South China National Botanical Garden, Guangzhou, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chao Yang
- State Key Laboratory of Plant Diversity and Specialty Crops, Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, South China National Botanical Garden, Guangzhou, China
- College of Life Science, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Yuling Zhao
- Jinghe County Goji Industrial Development Center, Jinghe County, Xinjiang Uygur Autonomous Region, China
| | - Ying Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, South China National Botanical Garden, Guangzhou, China
- College of Life Science, Gannan Normal University, Ganzhou, Jiangxi, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
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Timkin PD, Penzin AA. Bioinformatic method for determining single nucleotide polymorphisms on the example of gene <i>WIN</i> in <i>Glycine max</i>. PROCEEDINGS OF UNIVERSITIES. APPLIED CHEMISTRY AND BIOTECHNOLOGY 2023. [DOI: 10.21285/2227-2925-2022-12-4-599-604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
In this paper, a hypothetical method for locating SNPs (single nucleotide polymorphisms) on the example of the ribonuclease gene WIN was proposed. Ribonuclease comprises an enzyme that participates in defence reactions against fungal infections in soybeans, as well as other protective responses to biotic stress. Its belonging to the RNA-ases group determines the specific properties, namely the ability to degrade foreign nucleic acids. This ability provides for a general nonspecific immune response of the plant to the invasion of antigenic structures. Modern biotechnology calls for the development of molecular methods and approaches that will increase the resistance of a culture or accelerate the processes of its adaptation in the field. This problem can be solved by using technologies of SNP artificial induction in those parts of the genome that encode proteins capable of acting in protective reactions against biotic stress. In the study, 5 single-nucleotide polymorphisms were proposed using bioinformatic analysis. Since the localisation and detection of SNPs comprise a challenging task due to the presence of a single nucleotide change, in the biotechnological practice, predictive analysis is carried out in order to localise the potential sequence of occurring single-nucleotide polymorphism. Following the identification of the hypothetical SNP location, they can be further detected using complex molecular methods, such as real-time PCR or local sequencing. This technology can become a powerful tool for breeding soybean varieties having predetermined properties. Such theoretical and predictive models will allow for a quicker response to the dynamic environment under manmade load on plants.
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Akbari M, Sabouri H, Sajadi SJ, Yarahmadi S, Ahangar L, Abedi A, Katouzi M. Mega Meta-QTLs: A Strategy for the Production of Golden Barley (Hordeum vulgare L.) Tolerant to Abiotic Stresses. Genes (Basel) 2022; 13:genes13112087. [PMID: 36360327 PMCID: PMC9690463 DOI: 10.3390/genes13112087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/06/2022] [Accepted: 11/07/2022] [Indexed: 11/12/2022] Open
Abstract
Abiotic stresses cause a significant decrease in productivity and growth in agricultural products, especially barley. Breeding has been considered to create resistance against abiotic stresses. Pyramiding genes for tolerance to abiotic stresses through selection based on molecular markers connected to Mega MQTLs of abiotic tolerance can be one of the ways to reach Golden Barley. In this study, 1162 original QTLs controlling 116 traits tolerant to abiotic stresses were gathered from previous research and mapped from various populations. A consensus genetic map was made, including AFLP, SSR, RFLP, RAPD, SAP, DArT, EST, CAPS, STS, RGA, IFLP, and SNP markers based on two genetic linkage maps and 26 individual linkage maps. Individual genetic maps were created by integrating individual QTL studies into the pre-consensus map. The consensus map covered a total length of 2124.43 cM with an average distance of 0.25 cM between markers. In this study, 585 QTLs and 191 effective genes related to tolerance to abiotic stresses were identified in MQTLs. The most overlapping QTLs related to tolerance to abiotic stresses were observed in MQTL6.3. Furthermore, three MegaMQTL were identified, which explained more than 30% of the phenotypic variation. MQTLs, candidate genes, and linked molecular markers identified are essential in barley breeding and breeding programs to develop produce cultivars resistant to abiotic stresses.
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Affiliation(s)
- Mahjoubeh Akbari
- Department of Plant Production, Collage of Agriculture Science and Natural Resource, Gonbad Kavous University, Gonbad-e Kavus 4971799151, Iran
| | - Hossein Sabouri
- Department of Plant Production, Collage of Agriculture Science and Natural Resource, Gonbad Kavous University, Gonbad-e Kavus 4971799151, Iran
- Correspondence: (H.S.); (M.K.); Tel.: +98-9111438917 (H.S.); +41-779660486 (M.K.)
| | - Sayed Javad Sajadi
- Department of Plant Production, Collage of Agriculture Science and Natural Resource, Gonbad Kavous University, Gonbad-e Kavus 4971799151, Iran
| | - Saeed Yarahmadi
- Horticulture-Crops Reseaech Department, Golestan Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Gorgan 4969186951, Iran
| | - Leila Ahangar
- Department of Plant Production, Collage of Agriculture Science and Natural Resource, Gonbad Kavous University, Gonbad-e Kavus 4971799151, Iran
| | - Amin Abedi
- Department of Plant Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht 4199613776, Iran
| | - Mahnaz Katouzi
- Crop Génome Dynamics Group, Agroscope Changins, 1260 Nyon, Switzerland
- Correspondence: (H.S.); (M.K.); Tel.: +98-9111438917 (H.S.); +41-779660486 (M.K.)
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Alptekin B, Erfatpour M, Mangel D, Pauli D, Blake T, Turner H, Lachowiec J, Sherman J, Fischer A. Selection of favorable alleles of genes controlling flowering and senescence improves malt barley quality. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:59. [PMID: 37313013 PMCID: PMC10248683 DOI: 10.1007/s11032-022-01331-7] [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: 04/07/2022] [Accepted: 09/14/2022] [Indexed: 06/15/2023]
Abstract
Malt barley (Hordeum vulgare L.) is an important cash crop with stringent grain quality standards. Timing of the switch from vegetative to reproductive growth and timing of whole-plant senescence and nutrient remobilization are critical for cereal grain yield and quality. Understanding the genetic variation in genes associated with these developmental traits can streamline genotypic selection of superior malt barley germplasm. Here, we determined the effects of allelic variation in three genes encoding a glycine-rich RNA-binding protein (HvGR-RBP1) and two NAC transcription factors (HvNAM1 and HvNAM2) on malt barley agronomics and quality using previously developed markers for HvGR-RBP1 and HvNAM1 and a novel marker for HvNAM2. Based on a single-nucleotide polymorphism (SNP) in the first intron, the utilized marker differentiates NAM2 alleles of low-grain protein variety 'Karl' and of higher protein variety 'Lewis'. We demonstrate that the selection of favorable alleles for each gene impacts heading date, senescence timing, grain size, grain protein concentration, and malt quality. Specifically, combining 'Karl' alleles for the two NAC genes with the 'Lewis' HvGR-RBP1 allele extends grain fill duration, increases the percentage of plump kernels, decreases grain protein, and provides malt quality stability. Molecular markers for these genes are therefore highly useful tools in malt barley breeding. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01331-7.
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Affiliation(s)
- Burcu Alptekin
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717 USA
- Present Address: Department of Bacteriology, University of Wisconsin, Madison, WI 53706 USA
| | - Mohammad Erfatpour
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717 USA
- Present Address: Department of Plant Sciences, North Dakota State University, Fargo, ND 58108 USA
| | - Dylan Mangel
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717 USA
- Present Address: Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
| | - Duke Pauli
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717 USA
- Present Address: School of Plant Sciences, University of Arizona, Tucson, AZ 85721 USA
| | - Tom Blake
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717 USA
| | - Hannah Turner
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717 USA
| | - Jennifer Lachowiec
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717 USA
| | - Jamie Sherman
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717 USA
| | - Andreas Fischer
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717 USA
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Trubacheeva NV, Pershina LA. Problems and possibilities of studying malting quality in barley using molecular genetic approaches. Vavilovskii Zhurnal Genet Selektsii 2021; 25:171-177. [PMID: 34901715 PMCID: PMC8627870 DOI: 10.18699/vj21.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/24/2020] [Accepted: 10/26/2020] [Indexed: 11/19/2022] Open
Abstract
About one-third of the world’s barley crop is used for malt production to meet the needs of the brewing
industry. In this regard, the study of the genetic basis of malting quality traits and the breeding of malting barley
varieties that are adaptive to their growing conditions are relevant throughout the world, particularly in the Russian Federation, where the cultivation and use of foreign malting varieties of barley prevails. The main parameters
of malting quality (artificially germinated and dried barley grains) are malt extract, diastatic power, Kolbach index,
viscosity, grain protein, wort β-glucan, free amino nitrogen, and soluble protein content. Most of these components
are under the control of quantitative trait loci (QTLs) and are affected by environmental conditions, which complicates their study and precise localization. In addition, the phenotypic assessment of malting quality traits requires
elaborate, expensive phenotypic analyses. Currently, there are more than 200 QTLs associated with malting parameters, which were identified using biparental mapping populations. Molecular markers are widely used both for
mapping QTL loci responsible for malting quality traits and for performing marker-assisted selection (MAS), which,
in combination with conventional breeding, makes it possible to create effective strategies aimed at accelerating
the process of obtaining new promising genotypes. Nevertheless, the MAS of malting quality traits faces a series of
difficulties, such as the low accuracy of localization of QTLs, their ineffectiveness when transferred to another genetic background, and linkage with undesirable traits, which makes it necessary to validate QTLs and the molecular
markers linked to them. This review presents the results of studies that used MAS to improve the malting quality of
barley, and it also considers studies that searched for associations between genotype and phenotype, carried out
using GWAS (genome-wide association study) approaches based on the latest achievements of high-throughput
genotyping (diversity array technology (DArT) and single-nucleotide polymorphism markers (SNPs)).
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Affiliation(s)
- N V Trubacheeva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Kurchatov Genomics Center of ICG SB RAS, Novosibirsk, Russia
| | - L A Pershina
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Kurchatov Genomics Center of ICG SB RAS, Novosibirsk, Russia
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Identification and characterization of mRNAs and lncRNAs of a barley shrunken endosperm mutant using RNA-seq. Genetica 2020; 148:55-68. [PMID: 32078720 DOI: 10.1007/s10709-020-00087-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 02/13/2020] [Indexed: 01/03/2023]
Abstract
Barley shrunken endosperm mutants have been extensively reported. However, knowledge of the underlying molecular mechanisms of these mutants remains limited. Here, a pair of near isogenic lines (normal endosperm: Bowman and shrunken endosperm: sex1) was subjected to transcriptome analysis to identify mRNAs and lncRNAs related to endosperm development to further dissect its mechanism of molecular regulation. A total of 2123 (1140 up- and 983 down-regulated) unique differentially expressed genes (DEGs) were detected. Functional analyses showed that these DEGs were mainly involved in starch and sucrose metabolism, biosynthesis of secondary metabolites, and plant hormone signal transduction. A total of 343 unique target genes were identified for 57 differentially expressed lncRNAs (DE lncRNAs). These DE lncRNAs were mainly involved in glycerophospholipid metabolism, starch and sucrose metabolism, hormone signal transduction, and stress response. In addition, key lncRNAs were identified by constructing a co-expression network of the target genes of DE lncRNAs. Transcriptome results suggested that mRNA and lncRNA played a critical role in endosperm development. The shrunken endosperm in barley seems to be closely related to plant hormone signal transduction, starch and sucrose metabolism, and cell apoptosis. This study provides a foundation for fine mapping, elucidates the molecular mechanism of shrunken endosperm mutants, and also provides a reference for further studies of lncRNAs during the grain development of plants.
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Gao Y, de Bang TC, Schjoerring JK. Cisgenic overexpression of cytosolic glutamine synthetase improves nitrogen utilization efficiency in barley and prevents grain protein decline under elevated CO 2. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1209-1221. [PMID: 30525274 PMCID: PMC6576097 DOI: 10.1111/pbi.13046] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 10/23/2018] [Accepted: 11/09/2018] [Indexed: 05/23/2023]
Abstract
Cytosolic glutamine synthetase (GS1) plays a central role in nitrogen (N) metabolism. The importance of GS1 in N remobilization during reproductive growth has been reported in cereal species but attempts to improve N utilization efficiency (NUE) by overexpressing GS1 have yielded inconsistent results. Here, we demonstrate that transformation of barley (Hordeum vulgare L.) plants using a cisgenic strategy to express an extra copy of native HvGS1-1 lead to increased HvGS1.1 expression and GS1 enzyme activity. GS1 overexpressing lines exhibited higher grain yields and NUE than wild-type plants when grown under three different N supplies and two levels of atmospheric CO2 . In contrast with the wild-type, the grain protein concentration in the GS1 overexpressing lines did not decline when plants were exposed to elevated (800-900 μL/L) atmospheric CO2 . We conclude that an increase in GS1 activity obtained through cisgenic overexpression of HvGS1-1 can improve grain yield and NUE in barley. The extra capacity for N assimilation obtained by GS1 overexpression may also provide a means to prevent declining grain protein levels under elevated atmospheric CO2 .
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Affiliation(s)
- Yajie Gao
- Department of Plant and Environmental SciencesFaculty of ScienceCopenhagen UniversityFrederiksbergDenmark
| | - Thomas C. de Bang
- Department of Plant and Environmental SciencesFaculty of ScienceCopenhagen UniversityFrederiksbergDenmark
| | - Jan K. Schjoerring
- Department of Plant and Environmental SciencesFaculty of ScienceCopenhagen UniversityFrederiksbergDenmark
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Chai L, Chen Z, Bian R, Zhai H, Cheng X, Peng H, Yao Y, Hu Z, Xin M, Guo W, Sun Q, Zhao A, Ni Z. Dissection of two quantitative trait loci with pleiotropic effects on plant height and spike length linked in coupling phase on the short arm of chromosome 2D of common wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1815-1831. [PMID: 30915484 PMCID: PMC6531420 DOI: 10.1007/s00122-019-03318-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 09/14/2018] [Indexed: 05/10/2023]
Abstract
KEY MESSAGE Two QTL with pleiotropic effects on plant height and spike length linked in coupling phase on chromosome 2DS were dissected, and diagnostic marker for each QTL was developed. Plant height (PHT) is a crucial trait related to plant architecture and yield potential, and dissection of its underlying genetic basis would help to improve the efficiency of designed breeding in wheat. Here, two quantitative trait loci (QTL) linked in coupling phase on the short arm of chromosome 2D with pleiotropic effects on PHT and spike length, QPht/Sl.cau-2D.1 and QPht/Sl.cau-2D.2, were separated and characterized. QPht/Sl.cau-2D.1 is a novel QTL located between SNP makers BS00022234_51 and BobWhite_rep_c63957_1472. QPht/Sl.cau-2D.2 is mapped between two SSR markers, SSR-2062 and Xgwm484, which are located on the same genomic interval as Rht8. Moreover, the diagnostic marker tightly linked with each QTL was developed for the haplotype analysis using diverse panels of wheat accessions. The frequency of the height-reduced allele of QPht/Sl.cau-2D.1 is much lower than that of QPht/Sl.cau-2D.2, suggesting that this novel QTL may be an attractive target for genetic improvement. Consistent with a previous study of Rht8, a significant difference in cell length was observed between the NILs of QPht/Sl.cau-2D.2. By contrast, there was no difference in cell length between NILs of QPht/Sl.cau-2D.1, indicating that the underlying molecular mechanism for these two QTL may be different. Collectively, these data provide a new example of QTL dissection, and the developed diagnostic markers will be useful in marker-assisted pyramiding of QPht/Sl.cau-2D.1 and/or QPht/Sl.cau-2D.2 with the other genes in wheat breeding.
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Affiliation(s)
- Lingling Chai
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Zhaoyan Chen
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Ruolin Bian
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Huijie Zhai
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xuejiao Cheng
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Weilong Guo
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Aiju Zhao
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture/Forestry Sciences, Hebei Crop Genetic Breeding Laboratory, Shijiazhuang, 050035, China.
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality, China Agricultural University, Beijing, 100193, China.
- National Plant Gene Research Centre, Beijing, 100193, China.
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Chattopadhyay K, Behera L, Bagchi TB, Sardar SS, Moharana N, Patra NR, Chakraborti M, Das A, Marndi BC, Sarkar A, Ngangkham U, Chakraborty K, Bose LK, Sarkar S, Ray S, Sharma S. Detection of stable QTLs for grain protein content in rice (Oryza sativa L.) employing high throughput phenotyping and genotyping platforms. Sci Rep 2019; 9:3196. [PMID: 30824776 PMCID: PMC6397320 DOI: 10.1038/s41598-019-39863-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 01/30/2019] [Indexed: 11/10/2022] Open
Abstract
Lack of appropriate donors, non-utilization of high throughput phenotyping and genotyping platforms with high genotype × environment interaction restrained identification of robust QTLs for grain protein content (GPC) in rice. In the present investigation a BC3F4 mapping population was developed using grain protein donor, ARC10075 and high-yielding cultivar Naveen and 190 lines were genotyped using 40 K Affimetrix custom SNP array with the objective to identify stable QTLs for protein content. Three of the identified QTLs, one for GPC (qGPC1.1) and the other two for single grain protein content (qSGPC2.1, qSGPC7.1) were stable over the environments explaining 13%, 14% and 7.8% of the phenotypic variances, respectively. Stability and repeatability of these additive QTLs were supported by the synergistic additive effects of multi-environmental-QTLs. One epistatic-QTL, independent of the main effect QTL was detected over the environment for SGPC. A few functional genes governing seed storage protein were hypothesised inside these identified QTLs. The qGPC1.1 was validated by NIR Spectroscopy-based high throughput phenotyping in BC3F5 population. Higher glutelin content was estimated in high-protein lines with the introgression of qGPC1.1 in telomeric region of short arm of chromosome 1. This was supported by the postulation of probable candidate gene inside this QTL region encoding glutelin family proteins.
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Affiliation(s)
| | | | | | | | | | | | | | - Avijit Das
- ICAR-National Institute of Natural Fibre Engineering and Technology, Kolkata, India
| | | | - Ananta Sarkar
- ICAR- Central Institute for Women in Agriculture, Bhubaneswar, India
| | | | | | | | - Sutapa Sarkar
- ICAR-National Rice Research Institute, Cuttack, India
| | - Soham Ray
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, India
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Chai L, Chen Z, Bian R, Zhai H, Cheng X, Peng H, Yao Y, Hu Z, Xin M, Guo W, Sun Q, Zhao A, Ni Z. Dissection of two quantitative trait loci with pleiotropic effects on plant height and spike length linked in coupling phase on the short arm of chromosome 2D of common wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2621-2637. [PMID: 30267114 DOI: 10.1007/s00122-018-3177-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/01/2018] [Indexed: 06/08/2023]
Abstract
Two QTL with pleiotropic effects on plant height and spike length linked in coupling phase on chromosome 2DS were dissected, and diagnostic marker for each QTL was developed. Plant height (PHT) is a crucial trait related to plant architecture and yield potential, and dissection of its underlying genetic basis would help to improve the efficiency of designed breeding in wheat. Here, two quantitative trait loci (QTL) linked in coupling phase on the short arm of chromosome 2D with pleiotropic effects on PHT and spike length, QPht/Sl.cau-2D.1 and QPht/Sl.cau-2D.2, were separated and characterized. QPht/Sl.cau-2D.1 is a novel QTL located between SNP makers BS00022234_51 and BobWhite_rep_c63957_1472. QPht/Sl.cau-2D.2 is mapped between two SSR markers, SSR-2062 and Xgwm484, which are located on the same genomic interval as Rht8. Moreover, the diagnostic marker tightly linked with each QTL was developed for the haplotype analysis using diverse panels of wheat accessions. The frequency of the height-reduced allele of QPht/Sl.cau-2D.1 is much lower than that of QPht/Sl.cau-2D.2, suggesting that this novel QTL may be an attractive target for genetic improvement. Consistent with a previous study of Rht8, a significant difference in cell length was observed between the NILs of QPht/Sl.cau-2D.2. By contrast, there was no difference in cell length between NILs of QPht/Sl.cau-2D.1, indicating that the underlying molecular mechanism for these two QTL may be different. Collectively, these data provide a new example of QTL dissection, and the developed diagnostic markers will be useful in marker-assisted pyramiding of QPht/Sl.cau-2D.1 and/or QPht/Sl.cau-2D.2 with the other genes in wheat breeding.
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Affiliation(s)
- Lingling Chai
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Zhaoyan Chen
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Ruolin Bian
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Huijie Zhai
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xuejiao Cheng
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Weilong Guo
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Aiju Zhao
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture/Forestry Sciences, Hebei Crop Genetic Breeding Laboratory, Shijiazhuang, 050035, China.
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality, China Agricultural University, Beijing, 100193, China.
- National Plant Gene Research Centre, Beijing, 100193, China.
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Yao X, Wu K, Yao Y, Bai Y, Ye J, Chi D. Construction of a high-density genetic map: genotyping by sequencing (GBS) to map purple seed coat color ( Psc) in hulless barley. Hereditas 2018; 155:37. [PMID: 30473656 PMCID: PMC6240233 DOI: 10.1186/s41065-018-0072-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/18/2018] [Indexed: 01/24/2023] Open
Abstract
Background Colored hulless barley are more suitable in food processing compared to normal (yellow) varieties because it is rich in bioactive compounds and produces higher extraction pearling fractions. Therefore, seed coat color is an important agronomic trait for the breeding and study of hulless barley. Results Genotyping-by-sequencing single-nucleotide polymorphism (GBS-SNP) analysis of a doubled haploid (DH) mapping population (Nierumuzha × Kunlun10) was conducted to map the purple seed coat color genes (Psc). A high-density genetic map of hulless barley was constructed, which contains 3662 efficient SNP markers with 1129 bin markers. Seven linkage groups were resolved, which had a total length of 645.56 cM. Chromosome length ranged from 60.21 cM to 127.21 cM, with average marker density of 0.57 cM. A total of five loci accounting for 3.79% to 23.86% of the observed phenotypic variation for Psc were detected using this high-density map. Five structural candidate genes (F3’M, HID, UF3GT, UFGT and 5MAT) and one regulatory factor (Ant1) related to flavonoid or anthocyanin biosynthesis were identified.. Conclusions Five structural candidate genes and one regulatory factor related to flavonoid or anthocyanin biosynthesis have been identified using a high-density genetic map of hulless barley. This study lays the foundation for map-based cloning of Psc but provides a valuable tool for studying marker-trait associations and its application to marker-assisted breeding of hulless barley. Electronic supplementary material The online version of this article (10.1186/s41065-018-0072-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaohua Yao
- 1State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016 China.,2Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016 China.,Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, 810016 China.,Qinghai Subcenter of National Hulless Barley Improvement, Xining, 810016 China
| | - Kunlun Wu
- 1State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016 China.,2Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016 China.,Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, 810016 China.,Qinghai Subcenter of National Hulless Barley Improvement, Xining, 810016 China
| | - Youhua Yao
- 1State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016 China.,2Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016 China.,Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, 810016 China.,Qinghai Subcenter of National Hulless Barley Improvement, Xining, 810016 China
| | - Yixiong Bai
- 1State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016 China.,2Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016 China.,Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, 810016 China.,Qinghai Subcenter of National Hulless Barley Improvement, Xining, 810016 China
| | - Jingxiu Ye
- 1State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016 China.,2Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016 China
| | - Dezhao Chi
- 1State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016 China.,2Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016 China.,Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, 810016 China.,Qinghai Subcenter of National Hulless Barley Improvement, Xining, 810016 China
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12
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Che Y, Song N, Yang Y, Yang X, Duan Q, Zhang Y, Lu Y, Li X, Zhang J, Li X, Zhou S, Li L, Liu W. QTL Mapping of Six Spike and Stem Traits in Hybrid Population of Agropyron Gaertn. in Multiple Environments. FRONTIERS IN PLANT SCIENCE 2018; 9:1422. [PMID: 30425721 PMCID: PMC6218563 DOI: 10.3389/fpls.2018.01422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 09/06/2018] [Indexed: 05/31/2023]
Abstract
Most Agropyron Gaertn. species are excellent sources of forage. The derivative lines of wheat-Agropyron cristatum show elite agronomic traits, and some are valuable for wheat breeding. The species of Agropyron Gaertn. was mainly recognized by the spike morphology in traditional taxon. Six traits, including spike length (SL), ear stem length (ESL), the second internodes length (SIL), spikelet number per spike (SNS), floret number per spikelet (FNS), and grain number per spikelet (GNS), are vital to morphology studies and also influences the forage crop yield. To elucidate the genetic basis of spike and stem traits, a quantitative trait locus (QTL) analysis was conducted in a cross-pollinated (CP) hybrid population derived from a cross between two diverse parents, Agropyron mongolicum Keng Z2098 and A. cristatum (L.) Gaertn. Z1842, evaluated across three ecotopes (Langfang, Changli, and Guyuan of Hebei, China) over 3 years (from 2014 to 2016). Construction of a high-density linkage map was based on 1,023 single-nucleotide polymorphism (SNP) markers, covering 907.8 cM of the whole Agropyron genome. A total of 306 QTLs with single QTL in different environments explaining 0.07-33.21% of the phenotypic variation were detected for study traits. Seven major-effect QTLs were identified, including one for ESL on chromosome 3, one for SIL on chromosome 5, three for SL (two on chromosome 2 and one on chromosome 4), and two for SNS on chromosomes 3 and 7. Also, seven stable QTLs, including four for ESL, one for SL, one for GNS, and one for FNS, were mainly mapped on chromosomes 2, 3, 4, 5, and 7, respectively, elucidating 0.25-14.98% of the phenotypic variations. On the use of Agropyron CP hybrid population to identify QTL determining spike and stem traits for the first time, these QTLs for six traits would provide a theoretical reference for the molecular marker-assisted selection in the improvement of forage and cereal crop species.
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Affiliation(s)
- Yonghe Che
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Nan Song
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yanping Yang
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Xinming Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qingqing Duan
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuqing Lu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuqing Li
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Jinpeng Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiuquan Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shenghui Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lihui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weihua Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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