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Ren J, Li W, Guo Z, Ma Z, Wan D, Lu S, Guo L, Gou H, Chen B, Mao J. Whole-genome resequencing and transcriptome analyses of four generation mutants to reveal spur-type and skin-color related genes in apple (Malus domestica Borkh. Cv. Red delicious). BMC PLANT BIOLOGY 2023; 23:607. [PMID: 38030998 PMCID: PMC10688089 DOI: 10.1186/s12870-023-04631-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 11/24/2023] [Indexed: 12/01/2023]
Abstract
BACKGROUND Bud sport is a kind of somatic mutation that usually occurred in apple. 'Red Delicious' is considered to be a special plant material of bud sport, whereas the genetic basis of plant mutants is still unknown. In this study, we used whole-genome resequencing and transcriptome sequencing to identify genes related to spur-type and skin-color in the 'Red Delicious' (G0) and its four generation mutants including 'Starking Red' (G1), 'Starkrimson' (G2), 'Campbell Redchief' (G3) and 'Vallee Spur' (G4). RESULTS The number of single nucleotide polymorphisms (SNPs), insertions and deletions (InDels) and structural variations (SVs) were decreased in four generation mutants compared to G0, and the number of unique SNPs and InDels were over 9-fold and 4-fold higher in G1 versus (vs.) G2 and G2 vs. G3, respectively. Chromosomes 2, 5, 11 and 15 carried the most SNPs, InDels and SVs, while chromosomes 1 and 6 carried the least. Meanwhile, we identified 4,356 variation genes by whole-genome resequencing and transcriptome, and obtained 13 and 16 differentially expressed genes (DEGs) related to spur-type and skin-color by gene expression levels. Among them, DELLA and 4CL7 were the potential genes that regulate the difference of spur-type and skin-color characters, respectively. CONCLUSIONS Our study identified potential genes associated with spur-type and skin-color differences in 'Red Delicious' and its four generation mutants, which provides a theoretical foundation for the mechanism of the apple bud sport.
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Affiliation(s)
- Jiaxuan Ren
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Wenfang Li
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Zhigang Guo
- Tianshui Normal University, Tianshui, 741001, PR China
| | - Zonghuan Ma
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Dongshi Wan
- College of Ecology, Lanzhou University, Lanzhou, 730000, PR China
| | - Shixiong Lu
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Lili Guo
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Huimin Gou
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Baihong Chen
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China.
| | - Juan Mao
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China.
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Guo N, Han S, Zong M, Wang G, Duan M, Liu F. Construction and Application of an F1-Derived Doubled-Haploid Population and High-Density Genetic Map for Ornamental Kale Breeding. Genes (Basel) 2023; 14:2104. [PMID: 38003047 PMCID: PMC10670981 DOI: 10.3390/genes14112104] [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: 10/08/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
Ornamental kale (Brassica oleracea var. acephala) is an attractive ornamental plant with a range of leaf colors and shapes. Breeding new varieties of ornamental kale has proven challenging due to its lengthy breeding cycle and the limited availability of genetic markers. In this study, a F1DH ornamental kale population comprising 300 DH lines was constructed using microspore culture. A high-density genetic map was developed by conducting whole-genome sequencing on 150 individuals from the F1DH population. The genetic map contained 1696 bin markers with 982,642 single-nucleotide polymorphisms (SNPs) spanning a total distance of 775.81 cM on all nine chromosomes with an average distance between markers of 0.46 cM. The ornamental kale genetic map contained substantially more SNP markers compared with published genetic maps for other B. oleracea crops. Furthermore, utilizing this high-density genetic map, we identified seven quantitative trait loci (QTLs) that significantly influence the leaf shape of ornamental kale. These findings are valuable for understanding the genetic basis of key agronomic traits in ornamental kale. The F1DH progenies provide an excellent resource for germplasm innovation and breeding new varieties of ornamental kale. Additionally, the high-density genetic map provides crucial insights for gene mapping and unraveling the molecular mechanisms behind important agronomic traits in ornamental kale.
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Affiliation(s)
| | | | | | | | | | - Fan Liu
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasms Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (N.G.); (S.H.); (M.Z.); (G.W.); (M.D.)
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Yang T, Amanullah S, Li S, Cheng R, Zhang C, Zhao Z, Liu H, Luan F, Wang X. Molecular Mapping of Putative Genomic Regions Controlling Fruit and Seed Morphology of Watermelon. Int J Mol Sci 2023; 24:15755. [PMID: 37958737 PMCID: PMC10650541 DOI: 10.3390/ijms242115755] [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: 10/04/2023] [Revised: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
The genetic regulatory basis of qualitative and quantitative phenotypes of watermelon is being investigated in different types of molecular and genetic breeding studies around the world. In this study, biparental F2 mapping populations were developed over two experimental years, and the collected datasets of fruit and seed traits exhibited highly significant correlations. Whole-genome resequencing of comparative parental lines was performed and detected single nucleotide polymorphism (SNP) loci were converted into cleaved amplified polymorphic sequence (CAPS) markers. The screened polymorphic markers were genotyped in segregating populations and two genetic linkage maps were constructed, which covered a total of 2834.28 and 2721.45 centimorgan (cM) genetic lengths, respectively. A total of 22 quantitative trait loci (QTLs) for seven phenotypic traits were mapped; among them, five stable and major-effect QTLs (PC-8-1, SL-9-1, SWi-9-1, SSi-9-1, and SW-6-1) and four minor-effect QTLs (PC-2-1 and PC-2-2; PT-2-1 and PT-2-2; SL-6-1 and SSi-6-2; and SWi-6-1 and SWi-6-2) were observed with 3.77-38.98% PVE. The adjacent QTL markers showed a good fit marker-trait association, and a significant allele-specific contribution was also noticed for genetic inheritance of traits. Further, a total of four candidate genes (Cla97C09G179150, Cla97C09G179350, Cla97C09G180040, and Cla97C09G180100) were spotted in the stable colocalized QTLs of seed size linked traits (SL-9-1 and SWi-9-1) that showed non-synonymous type mutations. The gene expression trends indicated that the seed morphology had been formed in the early developmental stage and showed the genetic regulation of seed shape formation. Hence, we think that our identified QTLs and genes would provide powerful genetic insights for marker-assisted breeding aimed at improving the quality traits of watermelon.
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Affiliation(s)
- Tiantian Yang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (R.C.); (Z.Z.); (H.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Sikandar Amanullah
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (R.C.); (Z.Z.); (H.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Shenglong Li
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (R.C.); (Z.Z.); (H.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Rui Cheng
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (R.C.); (Z.Z.); (H.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Chen Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (R.C.); (Z.Z.); (H.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Zhengxiang Zhao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (R.C.); (Z.Z.); (H.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Hongyu Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (R.C.); (Z.Z.); (H.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Feishi Luan
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (R.C.); (Z.Z.); (H.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Xuezheng Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (R.C.); (Z.Z.); (H.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
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Thummala SR, Guttikonda H, Tiwari S, Ramanan R, Baisakh N, Neelamraju S, Mangrauthia SK. Whole-Genome Sequencing of KMR3 and Oryza rufipogon-Derived Introgression Line IL50-13 (Chinsurah Nona 2/Gosaba 6) Identifies Candidate Genes for High Yield and Salinity Tolerance in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:810373. [PMID: 35712577 PMCID: PMC9197125 DOI: 10.3389/fpls.2022.810373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 04/04/2022] [Indexed: 06/15/2023]
Abstract
The genomes of an elite rice restorer line KMR3 (salinity-sensitive) and its salinity-tolerant introgression line IL50-13, a popular variety of coastal West Bengal, India, were sequenced. High-quality paired-end reads were obtained for KMR3 (147.6 million) and IL50-13 (131.4 million) with a sequencing coverage of 30X-39X. Scaffolds generated from the pre-assembled contigs of each sequenced genome were mapped separately onto the reference genome of Oryza sativa ssp. japonica cultivar Nipponbare to identify genomic variants in terms of SNPs and InDels. The SNPs and InDels identified for KMR3 and IL50-13 were then compared with each other to identify polymorphic SNPs and InDels unique and common to both the genomes. Functional enrichment analysis of the protein-coding genes with unique InDels identified GO terms involved in protein modification, ubiquitination, deubiquitination, peroxidase activity, and antioxidant activity in IL50-13. Linoleic acid metabolism, circadian rhythm, and alpha-linolenic acid metabolism pathways were enriched in IL50-13. These GO terms and pathways are involved in reducing oxidative damage, thus suggesting their role in stress responses. Sequence analysis of QTL markers or genes known to be associated with grain yield and salinity tolerance showed polymorphism in 20 genes, out of which nine were not previously reported. These candidate genes encoded Nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4 (NB-ARC) domain-containing protein, cyclase, receptor-like kinase, topoisomerase II-associated protein PAT1 domain-containing protein, ion channel regulatory protein, UNC-93 domain-containing protein, subunit A of the heteromeric ATP-citrate lyase, and three conserved hypothetical genes. Polymorphism was observed in the coding, intron, and untranslated regions of the genes on chromosomes 1, 2, 4, 7, 11, and 12. Genes showing polymorphism between the two genomes were considered as sequence-based new candidates derived from Oryza rufipogon for conferring high yield and salinity tolerance in IL50-13 for further functional studies.
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Affiliation(s)
| | | | - Shrish Tiwari
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | | | - Niranjan Baisakh
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
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Beerelli K, Balakrishnan D, Addanki KR, Surapaneni M, Rao Yadavalli V, Neelamraju S. Mapping of QTLs for Yield Traits Using F 2:3:4 Populations Derived From Two Alien Introgression Lines Reveals qTGW8.1 as a Consistent QTL for Grain Weight From Oryza nivara. FRONTIERS IN PLANT SCIENCE 2022; 13:790221. [PMID: 35356124 PMCID: PMC8959756 DOI: 10.3389/fpls.2022.790221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
Wild introgressions play a crucial role in crop improvement by transferring important novel alleles and broadening allelic diversity of cultivated germplasm. In this study, two stable backcross alien introgression lines 166s and 14s derived from Swarn/Oryza nivara IRGC81848 were used as parents to generate populations to map quantitative trait loci (QTLs) for yield-related traits. Field evaluation of yield-related traits in F2, F3, and F4 population was carried out in normal irrigated conditions during the wet season of 2015 and dry seasons of 2016 and 2018, respectively. Plant height, tiller number, productive tiller number, total dry matter, and harvest index showed a highly significant association to single plant yield in F2, F3, and F4. In all, 21, 30, and 17 QTLs were identified in F2, F2:3, and F2:4, respectively, for yield-related traits. QTLs qPH6.1 with 12.54% phenotypic variance (PV) in F2, qPH1.1 with 13.01% PV, qTN6.1 with 10.08% PV in F2:3, and qTGW6.1 with 15.19% PV in F2:4 were identified as major effect QTLs. QTLs qSPY4.1 and qSPY6.1 were detected for grain yield in F2 and F2:3 with PV 8.5 and 6.7%, respectively. The trait enhancing alleles of QTLs qSPY4.1, qSPY6.1, qPH1.1, qTGW6.1, qTGW8.1, qGN4.1, and qTDM5.1 were from O. nivara. QTLs of the yield contributing traits were found clustered in the same chromosomal region. qTGW8.1 was identified in a 2.6 Mb region between RM3480 and RM3452 in all three generations with PV 6.1 to 9.8%. This stable and consistent qTGW8.1 allele from O. nivara can be fine mapped for identification of causal genes. From this population, lines C212, C2124, C2128, and C2143 were identified with significantly higher SPY and C2103, C2116, and C2117 had consistently higher thousand-grain weight values than both the parents and Swarna across the generations and are useful in gene discovery for target traits and further crop improvement.
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Affiliation(s)
- Kavitha Beerelli
- National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, India
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, India
| | - Divya Balakrishnan
- National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Krishnam Raju Addanki
- National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, India
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, India
| | - Malathi Surapaneni
- National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | | | - Sarla Neelamraju
- National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, India
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Kim M, Xi H, Park J. Genome-wide comparative analyses of GATA transcription factors among 19 Arabidopsis ecotype genomes: Intraspecific characteristics of GATA transcription factors. PLoS One 2021; 16:e0252181. [PMID: 34038437 PMCID: PMC8153473 DOI: 10.1371/journal.pone.0252181] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 05/11/2021] [Indexed: 12/30/2022] Open
Abstract
GATA transcription factors (TFs) are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif (CX2CX17-20CX2C) followed by a basic region. Due to the low cost of genome sequencing, multiple strains of specific species have been sequenced: e.g., number of plant genomes in the Plant Genome Database (http://www.plantgenome.info/) is 2,174 originated from 713 plant species. Thus, we investigated GATA TFs of 19 Arabidopsis thaliana genome-widely to understand intraspecific features of Arabidopsis GATA TFs with the pipeline of GATA database (http://gata.genefamily.info/). Numbers of GATA genes and GATA TFs of each A. thaliana genome range from 29 to 30 and from 39 to 42, respectively. Four cases of different pattern of alternative splicing forms of GATA genes among 19 A. thaliana genomes are identified. 22 of 2,195 amino acids (1.002%) from the alignment of GATA domain amino acid sequences display variations across 19 ecotype genomes. In addition, maximally four different amino acid sequences per each GATA domain identified in this study indicate that these position-specific amino acid variations may invoke intraspecific functional variations. Among 15 functionally characterized GATA genes, only five GATA genes display variations of amino acids across ecotypes of A. thaliana, implying variations of their biological roles across natural isolates of A. thaliana. PCA results from 28 characteristics of GATA genes display the four groups, same to those defined by the number of GATA genes. Topologies of bootstrapped phylogenetic trees of Arabidopsis chloroplasts and common GATA genes are mostly incongruent. Moreover, no relationship between geographical distribution and their phylogenetic relationships was found. Our results present that intraspecific variations of GATA TFs in A. thaliana are conserved and evolutionarily neutral along with 19 ecotypes, which is congruent to the fact that GATA TFs are one of the main regulators for controlling essential mechanisms, such as seed germination and hypocotyl elongation.
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Affiliation(s)
- Mangi Kim
- InfoBoss Inc., Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Republic of Korea
| | - Hong Xi
- InfoBoss Inc., Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Republic of Korea
| | - Jongsun Park
- InfoBoss Inc., Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Republic of Korea
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Current Understanding of Leaf Senescence in Rice. Int J Mol Sci 2021; 22:ijms22094515. [PMID: 33925978 PMCID: PMC8123611 DOI: 10.3390/ijms22094515] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/21/2021] [Accepted: 04/24/2021] [Indexed: 11/17/2022] Open
Abstract
Leaf senescence, which is the last developmental phase of plant growth, is controlled by multiple genetic and environmental factors. Leaf yellowing is a visual indicator of senescence due to the loss of the green pigment chlorophyll. During senescence, the methodical disassembly of macromolecules occurs, facilitating nutrient recycling and translocation from the sink to the source organs, which is critical for plant fitness and productivity. Leaf senescence is a complex and tightly regulated process, with coordinated actions of multiple pathways, responding to a sophisticated integration of leaf age and various environmental signals. Many studies have been carried out to understand the leaf senescence-associated molecular mechanisms including the chlorophyll breakdown, phytohormonal and transcriptional regulation, interaction with environmental signals, and associated metabolic changes. The metabolic reprogramming and nutrient recycling occurring during leaf senescence highlight the fundamental role of this developmental stage for the nutrient economy at the whole plant level. The strong impact of the senescence-associated nutrient remobilization on cereal productivity and grain quality is of interest in many breeding programs. This review summarizes our current knowledge in rice on (i) the actors of chlorophyll degradation, (ii) the identification of stay-green genotypes, (iii) the identification of transcription factors involved in the regulation of leaf senescence, (iv) the roles of leaf-senescence-associated nitrogen enzymes on plant performance, and (v) stress-induced senescence. Compiling the different advances obtained on rice leaf senescence will provide a framework for future rice breeding strategies to improve grain yield.
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Lian Q, Fu Q, Xu Y, Hu Z, Zheng J, Zhang A, He Y, Wang C, Xu C, Chen B, Garcia-Mas J, Zhao G, Wang H. QTLs and candidate genes analyses for fruit size under domestication and differentiation in melon (Cucumis melo L.) based on high resolution maps. BMC PLANT BIOLOGY 2021; 21:126. [PMID: 33658004 PMCID: PMC7931605 DOI: 10.1186/s12870-021-02904-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/24/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Melon is a very important horticultural crop produced worldwide with high phenotypic diversity. Fruit size is among the most important domestication and differentiation traits in melon. The molecular mechanisms of fruit size in melon are largely unknown. RESULTS Two high-density genetic maps were constructed by whole-genome resequencing with two F2 segregating populations (WAP and MAP) derived from two crosses (cultivated agrestis × wild agrestis and cultivated melo × cultivated agrestis). We obtained 1,871,671 and 1,976,589 high quality SNPs that show differences between parents in WAP and MAP. A total of 5138 and 5839 recombination events generated 954 bins in WAP and 1027 bins in MAP with the average size of 321.3 Kb and 301.4 Kb respectively. All bins were mapped onto 12 linkage groups in WAP and MAP. The total lengths of two linkage maps were 904.4 cM (WAP) and 874.5 cM (MAP), covering 86.6% and 87.4% of the melon genome. Two loci for fruit size were identified on chromosome 11 in WAP and chromosome 5 in MAP, respectively. An auxin response factor and a YABBY transcription factor were inferred to be the candidate genes for both loci. CONCLUSION The high-resolution genetic maps and QTLs analyses for fruit size described here will provide a better understanding the genetic basis of domestication and differentiation, and provide a valuable tool for map-based cloning and molecular marker assisted breeding.
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Affiliation(s)
- Qun Lian
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Qiushi Fu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Yongyang Xu
- Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Zhicheng Hu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Jing Zheng
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Aiai Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Yuhua He
- Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Changsheng Wang
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Shanghai, 200000, China
| | - Chuanqiang Xu
- Shenyang Agricultural University, College of Horticulture, Shenyang, 110866, China
| | - Benxue Chen
- Design Gollege, Zhoukou Normal University, Zhoukou, 466000, China
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Barcelona, Spain
| | - Guangwei Zhao
- Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China.
| | - Huaisong Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
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Vishnukiran T, Neeraja CN, Jaldhani V, Vijayalakshmi P, Raghuveer Rao P, Subrahmanyam D, Voleti SR. A major pleiotropic QTL identified for yield components and nitrogen content in rice (Oryza sativa L.) under differential nitrogen field conditions. PLoS One 2020; 15:e0240854. [PMID: 33079957 PMCID: PMC7575116 DOI: 10.1371/journal.pone.0240854] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 10/04/2020] [Indexed: 11/22/2022] Open
Abstract
To identify the genomic regions for yield and NUE of rice genotypes and lines with promising yield under low N, a recombinant inbred population (RIL) developed between BPT5204 (a mega variety known for its quality) and PTB1 (variety with high NUE) was evaluated for consecutive wet and dry seasons under low nitrogen (LN) and recommended nitrogen (RN) field conditions. A set of 291 RILs were characterized for 24 traits related to leaf, agro-morphological, yield, N content and nitrogen use efficiency indices. More than 50 RILs were found promising with grain yield >10 g under LN. Parental polymorphism survey with 297 SSRs and selective genotyping revealed five genomic regions associated with yield under LN, which were further saturated with polymorphic SSRs. Thirteen promising SSRs were identified out of 144 marker trait associations under LN using single marker analysis. Composite interval mapping showed 37 QTL under LN with five pleiotropic QTL. A major stable pleiotropic (RM13201—RM13209) from PTB1 spanning 825.4 kb region associated with straw N % (SNP) in both treatments across seasons and yield and yield related traits in WS appears to be promising for the MAS. Another major QTL (RM13181-RM13201) was found to be associated with only relative trait parameters of biomass, grain and grain nitrogen. These two major pleiotropic QTL (RM13201-RM13209 and RM13181-RM13201) on chromosome 2 were characterized for their positive allele effect and could be deployed for the development of rice varieties with NUE.
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Affiliation(s)
- T. Vishnukiran
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - C. N. Neeraja
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
- * E-mail:
| | - V. Jaldhani
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - P. Vijayalakshmi
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - P. Raghuveer Rao
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - D. Subrahmanyam
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - S. R. Voleti
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
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Balakrishnan D, Surapaneni M, Yadavalli VR, Addanki KR, Mesapogu S, Beerelli K, Neelamraju S. Detecting CSSLs and yield QTLs with additive, epistatic and QTL×environment interaction effects from Oryza sativa × O. nivara IRGC81832 cross. Sci Rep 2020; 10:7766. [PMID: 32385410 PMCID: PMC7210974 DOI: 10.1038/s41598-020-64300-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 04/10/2020] [Indexed: 12/25/2022] Open
Abstract
Chromosome segment substitution lines (CSSLs) are useful tools for precise mapping of quantitative trait loci (QTLs) and the evaluation of gene action and interaction in inter-specific crosses. In this study, a set of 90 back cross lines at BC2F8 generation derived from Swarna x Oryza nivara IRGC81832 was evaluated for yield traits under irrigated conditions in wet seasons of 3 consecutive years. We identified a set of 70 chromosome segment substitution lines, using genotyping data from 140 SSR markers covering 94.4% of O. nivara genome. Among these, 23 CSSLs were significantly different for 7 traits. 22 QTLs were detected for 11 traits with 6.51 to 46.77% phenotypic variation in 90 BILs. Three pleiotropic genomic regions associated with yield traits were mapped on chromosomes 1, 8 and 11. The marker interval RM206-RM144 at chromosome 11 was recurrently detected for various yield traits. Ten QTLs were identified consistently in the three consecutive years of testing. Seventeen pairs of significant epistatic QTLs (E-QTLs) were detected for days to flowering, days to maturity and plant height. Chromosome segments from O. nivara contributed trait enhancing alleles. The significantly improved lines and the stable QTLs identified in this study are valuable resource for gene discovery and yield improvement.
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11
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Genetic and genomic analysis for cocoon yield traits in silkworm. Sci Rep 2020; 10:5682. [PMID: 32231221 PMCID: PMC7105477 DOI: 10.1038/s41598-020-62507-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 03/16/2020] [Indexed: 12/05/2022] Open
Abstract
Domestic species provides a powerful model for examining genetic mechanisms in the evolution of yield traits. The domestic silkworm (Bombyx mori) is an important livestock species in sericulture. While the mechanisms controlling cocoon yield are largely unknown. Here, using B. mori and its wild relative B. mandarina as intercross parents, 100 BC1 individuals were sequenced by restriction site-associated DNA sequencing (RAD-Seq). The linkage map contained 9,632 markers was constructed. We performed high-resolution quantitative trait locus (QTL) mapping for four cocoon yield traits. A total of 11 QTLs were identified, including one yield-enhancing QTL from wild silkworm. By integrating population genomics and transcriptomic analysis with QTLs, some favourable genes were revealed, including 14 domestication-related genes and 71 differentially expressed genes (DEGs) in the fifth-instar larval silk gland transcriptome between B. mori and B. mandarina. The relationships between the expression of two important candidate genes (KWMTBOMO04917 and KWMTBOMO12906) and cocoon yield were supported by quantitative real-time PCR (qPCR). Our results provide some new insights into the molecular mechanisms of complex yield traits in silkworm. The combined method might be an efficient approach for identifying putative causal genes in domestic livestock and wild relatives.
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12
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In Silico Identification of QTL-Based Polymorphic Genes as Salt-Responsive Potential Candidates through Mapping with Two Reference Genomes in Rice. PLANTS 2020; 9:plants9020233. [PMID: 32054112 PMCID: PMC7076550 DOI: 10.3390/plants9020233] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/03/2020] [Accepted: 02/05/2020] [Indexed: 11/16/2022]
Abstract
Recent advances in next generation sequencing have created opportunities to directly identify genetic loci and candidate genes for abiotic stress responses in plants. With the objective of identifying candidate genes within the previously identified QTL-hotspots, the whole genomes of two divergent cultivars for salt responses, namely At 354 and Bg 352, were re-sequenced using Illumina Hiseq 2500 100PE platform and mapped to Nipponbare and R498 genomes. The sequencing results revealed approximately 2.4 million SNPs and 0.2 million InDels with reference to Nipponbare while 1.3 million and 0.07 million with reference to R498 in two parents. In total, 32,914 genes were reported across all rice chromosomes of this study. Gene mining within QTL hotspots revealed 1236 genes, out of which 106 genes were related to abiotic stress. In addition, 27 abiotic stress-related genes were identified in non-QTL regions. Altogether, 32 genes were identified as potential genes containing polymorphic non-synonymous SNPs or InDels between two parents. Out of 10 genes detected with InDels, tolerant haplotypes of Os01g0581400, Os10g0107000, Os11g0655900, Os12g0622500, and Os12g0624200 were found in the known salinity tolerant donor varieties. Our findings on different haplotypes would be useful in developing resilient rice varieties for abiotic stress by haplotype-based breeding studies.
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13
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Dong C, Zhang L, Chen Z, Xia C, Gu Y, Wang J, Li D, Xie Z, Zhang Q, Zhang X, Gui L, Liu X, Kong X. Combining a New Exome Capture Panel With an Effective varBScore Algorithm Accelerates BSA-Based Gene Cloning in Wheat. FRONTIERS IN PLANT SCIENCE 2020; 11:1249. [PMID: 32903549 PMCID: PMC7438552 DOI: 10.3389/fpls.2020.01249] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/29/2020] [Indexed: 05/07/2023]
Abstract
The discovery of functional genes underlying agronomic traits is of great importance for wheat improvement. Here we designed a new wheat exome capture probe panel based on IWGSC RefSeq v1.0 genome sequence information and developed an effective algorithm, varBScore, that can sufficiently reduce the background noise in gene mapping and identification. An effective method, termed bulked segregant exome capture sequencing (BSE-Seq) for identifying causal mutations or candidate genes was established by combining the use of a newly designed wheat exome capture panel, sequencing of bulked segregant pools from segregating populations, and the robust algorithm varBScore. We evaluated the effectiveness of varBScore on SNP calling using the published dataset for mapping and cloning the yellow rust resistance gene Yr7 in wheat. Furthermore, using BSE-Seq, we rapidly identified a wheat yellow leaf mutant gene, ygl1, in an ethyl methanesulfonate (EMS) mutant population and found that a single mutation of G to A at 921 position in the wild type YGL1 gene encoding magnesium-chelatase subunit chlI caused the leaf yellowing phenotype. We further showed that mutation of YGL1 through CRISPR/Cas9 gene editing led to a yellow phenotype on the leaves of transgenic wheat, indicating that ygl1 is the correct causal gene responsible for the mutant phenotype. In summary, our approach is highly efficient for discovering causal mutations and gene cloning in wheat.
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Affiliation(s)
- Chunhao Dong
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement, MOA, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lichao Zhang
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement, MOA, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Lichao Zhang, ; Xu Liu, ; Xiuying Kong,
| | - Zhongxu Chen
- Department of Life Science, Chengdu Tcuni Technology, Chengdu, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Chuan Xia
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement, MOA, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongqiang Gu
- Western Regional Research, United States Department of Agriculture-Agricultural Research Service, Albany, CA, United States
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Danping Li
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement, MOA, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhencheng Xie
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement, MOA, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiang Zhang
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement, MOA, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xueying Zhang
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement, MOA, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lixuan Gui
- Department of Life Science, Chengdu Tcuni Technology, Chengdu, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Xu Liu
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement, MOA, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Lichao Zhang, ; Xu Liu, ; Xiuying Kong,
| | - Xiuying Kong
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement, MOA, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Lichao Zhang, ; Xu Liu, ; Xiuying Kong,
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14
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Sun BR, Fu CY, Fan ZL, Chen Y, Chen WF, Zhang J, Jiang LQ, Lv S, Pan DJ, Li C. Genomic and transcriptomic analysis reveal molecular basis of salinity tolerance in a novel strong salt-tolerant rice landrace Changmaogu. RICE (NEW YORK, N.Y.) 2019; 12:99. [PMID: 31883029 PMCID: PMC6934643 DOI: 10.1186/s12284-019-0360-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 12/19/2019] [Indexed: 05/14/2023]
Abstract
BACKGROUND Salt stress is an important factor that limits rice yield. We identified a novel, strongly salt tolerant rice landrace called Changmaogu (CMG) collected from a coastal beach of Zhanjiang, Guangdong Province, China. The salt tolerance of CMG was much better than that of the international recognized salt tolerant rice cultivar Pokkali in the germination and seedling stages. RESULTS To understand the molecular basis of salt tolerance in CMG, we performed BSA-seq for two extreme bulks derived from the cross between CMG and a cultivar sensitive to salt, Zhefu802. Transcriptomic sequencing was conducted for CMG at the germination and young seedling stages. Six candidate regions for salt tolerance were mapped on Chromosome 1 by BSA-seq using the extreme populations. Based on the polymorphisms identified between both parents, we detected 32 genes containing nonsynonymous coding single nucleotide polymorphisms (SNPs) and frameshift mutations in the open reading frame (ORF) regions. With transcriptomic sequencing, we detected a large number of differentially expressed genes (DEGs) at the germination and seedling stages under salt stress. KEGG analysis indicated two of 69 DEGs shared at the germination and seedling stages were significantly enriched in the pathway of carotenoid biosynthesis. Of the 169 overlapping DEGs among three sample points at the seedling stage, 13 and six DEGs were clustered into the pathways of ABA signal transduction and carotenoid biosynthesis, respectively. Of the 32 genes carrying sequence variation, only OsPP2C8 (Os01g0656200) was differentially expressed in the young seedling stage under salt stress and also showed sequence polymorphism in the ORFs between CMG and Zhefu802. CONCLUSION OsPP2C8 was identified as the target candidate gene for salinity tolerance in the seedling stage. This provides an important genetic resource for the breeding of novel salt tolerant rice cultivars.
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Affiliation(s)
- Bing-Rui Sun
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Chong-Yun Fu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Zhi-Lan Fan
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
| | - Yu Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
| | - Wen-Feng Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
| | - Jing Zhang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
| | - Li-Qun Jiang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
| | - Shuwei Lv
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
| | - Da-Jian Pan
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
| | - Chen Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
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15
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Kamal NM, Gorafi YSA, Abdelrahman M, Abdellatef E, Tsujimoto H. Stay-Green Trait: A Prospective Approach for Yield Potential, and Drought and Heat Stress Adaptation in Globally Important Cereals. Int J Mol Sci 2019; 20:E5837. [PMID: 31757070 PMCID: PMC6928793 DOI: 10.3390/ijms20235837] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/12/2019] [Accepted: 11/13/2019] [Indexed: 11/16/2022] Open
Abstract
The yield losses in cereal crops because of abiotic stress and the expected huge losses from climate change indicate our urgent need for useful traits to achieve food security. The stay-green (SG) is a secondary trait that enables crop plants to maintain their green leaves and photosynthesis capacity for a longer time after anthesis, especially under drought and heat stress conditions. Thus, SG plants have longer grain-filling period and subsequently higher yield than non-SG. SG trait was recognized as a superior characteristic for commercially bred cereal selection to overcome the current yield stagnation in alliance with yield adaptability and stability. Breeding for functional SG has contributed in improving crop yields, particularly when it is combined with other useful traits. Thus, elucidating the molecular and physiological mechanisms associated with SG trait is maybe the key to defeating the stagnation in productivity associated with adaptation to environmental stress. This review discusses the recent advances in SG as a crucial trait for genetic improvement of the five major cereal crops, sorghum, wheat, rice, maize, and barley with particular emphasis on the physiological consequences of SG trait. Finally, we provided perspectives on future directions for SG research that addresses present and future global challenges.
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Affiliation(s)
- Nasrein Mohamed Kamal
- Arid Land Research Center, Tottori University, 1390 Hamasaka, Tottori 680-0001, Japan; (Y.S.A.G.); (M.A.)
- Agricultural Research Corporation, Wad-Medani P.O. Box 126, Sudan
| | - Yasir Serag Alnor Gorafi
- Arid Land Research Center, Tottori University, 1390 Hamasaka, Tottori 680-0001, Japan; (Y.S.A.G.); (M.A.)
- Agricultural Research Corporation, Wad-Medani P.O. Box 126, Sudan
| | - Mostafa Abdelrahman
- Arid Land Research Center, Tottori University, 1390 Hamasaka, Tottori 680-0001, Japan; (Y.S.A.G.); (M.A.)
- Botany Department, Faculty of Science, Aswan University, Aswan 81528, Egypt
| | - Eltayb Abdellatef
- Commission for Biotechnology and Genetic Engineering, National Center for Research, Khartoum P.O. Box 6096, Sudan;
| | - Hisashi Tsujimoto
- Arid Land Research Center, Tottori University, 1390 Hamasaka, Tottori 680-0001, Japan; (Y.S.A.G.); (M.A.)
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16
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Li B, Zhao S, Dou J, Ali A, Gebremeskel H, Gao L, He N, Lu X, Liu W. Genetic mapping and development of molecular markers for a candidate gene locus controlling rind color in watermelon. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2741-2753. [PMID: 31286160 DOI: 10.1007/s00122-019-03384-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 06/19/2019] [Indexed: 06/09/2023]
Abstract
ClCG08G017810 (ClCGMenG) encoding a 2-phytyl-1,4-beta-naphthoquinone methyltransferase protein is associated with formation of dark green versus light green rind color in watermelon. Rind color is an important agronomic trait in watermelon [Citrullus lanatus (Thunb.) Matsum. and Nakai], but the underlying molecular mechanism for this trait is not fully known. In the present study, we identified a single locus on chromosome 8 accounting for watermelon rind color (dark green vs. light green). Genetic analysis of F1, F2, and BC1 populations derived from two parental lines (9904 with dark green rind and Handel with light green rind) revealed that the watermelon rind color (dark green vs. light green) is controlled by a single locus, and dark green is dominant to light green rind. Initial mapping revealed a region of interest spanning 2.07 Mb on chromosome 8. Genetic mapping with CAPS and SNP markers narrowed down the candidate region to 31.4 kb. Gene annotation of the corresponding region in the reference genome revealed the ClCG08G017810 gene sequence encoding the 2-phytyl-1,4-beta-naphthoquinone methyltransferase protein. The sequence alignment of the candidate gene with the two parental lines suggested a nonsynonymous SNP mutation in the coding region of ClCG08G017810, converting an arginine (R) to glycine (G). The SNP might be associated with rind color of 103 watermelon germplasm lines investigated in this study. The qRT-PCR analysis revealed higher expression of ClCG08G017810 in dark green rind than in light green rind. Therefore, ClCG08G017810 is a candidate gene associated with watermelon rind color. The present study facilitates marker-assisted selection useful for the development of cultivars with desirable rind color.
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Affiliation(s)
- Bingbing Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Shengjie Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Junling Dou
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Aslam Ali
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Haileslassie Gebremeskel
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Lei Gao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Nan He
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Xuqiang Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China.
| | - Wenge Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
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17
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Calleja-Rodriguez A, Li Z, Hallingbäck HR, Sillanpää MJ, Wu HX, Abrahamsson S, García-Gil MR. Analysis of phenotypic- and Estimated Breeding Values (EBV) to dissect the genetic architecture of complex traits in a Scots pine three-generation pedigree design. J Theor Biol 2019; 462:283-292. [PMID: 30423305 DOI: 10.1016/j.jtbi.2018.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 10/17/2018] [Accepted: 11/09/2018] [Indexed: 11/28/2022]
Abstract
In forest tree breeding, family-based Quantitative Trait Loci (QTL) studies are valuable as methods to dissect the complexity of a trait and as a source of candidate genes. In the field of conifer research, our study contributes to the evaluation of phenotypic and predicted breeding values for the identification of QTL linked to complex traits in a three-generation pedigree population in Scots pine (Pinus sylvestris L.). A total of 11 470 open pollinated F2-progeny trees established at three different locations, were measured for growth and adaptive traits. Breeding values were predicted for their 360 mothers, originating from a single cross of two grand-parents. A multilevel LASSO association analysis was conducted to detect QTL using genotypes of the mothers with the corresponding phenotypes and Estimated Breeding Values (EBV). Different levels of genotype-by-environment (G × E) effects among sites at different years, were detected for survival and height. Moderate-to-low narrow sense heritabilities and EBV accuracies were found for all traits and all sites. We identified 18 AFLPs and 12 SNPs to be associated with QTL for one or more traits. 62 QTL were significant with percentages of variance explained ranging from 1.7 to 18.9%. In those cases where the same marker was associated to a phenotypic or an ebvQTL, the ebvQTL always explained higher proportion of the variance, maybe due to the more accurate nature of Estimated Breeding Values (EBV). Two SNP-QTL showed pleiotropic effects for traits related with hardiness, seed, cone and flower production. Furthermore, we detected several QTL with significant effects across multiple ages, which could be considered as strong candidate loci for early selection. The lack of reproducibility of some QTL detected across sites may be due to environmental heterogeneity reflected by the genotype- and QTL-by-environment effects.
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Affiliation(s)
- Ainhoa Calleja-Rodriguez
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Science, Umeå SE-901 83, Sweden; Skogforsk, Box 3, Sävar SE-91821, Sweden
| | - Zitong Li
- Melbourne Integrative Genomics and School of Mathematics and Statistics, the University of Melbourne, Parkville, Victoria 3010, Australia; Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki FI-00014, Finland
| | - Henrik R Hallingbäck
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Science, Umeå SE-901 83, Sweden; Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Science, Uppsala SE-75007, Sweden
| | - Mikko J Sillanpää
- Department of Mathematical Sciences and Biocenter Oulu, University of Oulu, Oulu FI-90014, Finland
| | - Harry X Wu
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Science, Umeå SE-901 83, Sweden
| | | | - Maria Rosario García-Gil
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Science, Umeå SE-901 83, Sweden.
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18
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Diniz AL, Giordani W, Costa ZP, Margarido GRA, Perseguini JMKC, Benchimol-Reis LL, Chiorato AF, Garcia AAF, Vieira MLC. Evidence for Strong Kinship Influence on the Extent of Linkage Disequilibrium in Cultivated Common Beans. Genes (Basel) 2018; 10:E5. [PMID: 30583474 PMCID: PMC6356217 DOI: 10.3390/genes10010005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 12/15/2018] [Accepted: 12/18/2018] [Indexed: 01/05/2023] Open
Abstract
Phaseolus vulgaris is an important grain legume for human consumption. Recently, association mapping studies have been performed for the species aiming to identify loci underlying quantitative variation of traits. It is now imperative to know whether the linkage disequilibrium (LD) reflects the true association between a marker and causative loci. The aim of this study was to estimate and analyze LD on a diversity panel of common beans using ordinary r² and r2 extensions which correct bias due to population structure (rS²), kinship (rV²), and both (rVS²). A total of 10,362 single nucleotide polymorphisms (SNPs) were identified by genotyping by sequencing (GBS), and polymorphisms were found to be widely distributed along the 11 chromosomes. In terms of r2, high values of LD (over 0.8) were identified between SNPs located at opposite chromosomal ends. Estimates for rV² were lower than those for rS². Results for rV² and rVS² were similar, suggesting that kinship may also include information on population structure. Over genetic distance, LD decayed to 0.1 at a distance of 1 Mb for rVS². Inter-chromosomal LD was also evidenced. This study showed that LD estimates decay dramatically according to the population structure, and especially the degree of kinship. Importantly, the LD estimates reported herein may influence our ability to perform association mapping studies on P. vulgaris.
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Affiliation(s)
- Augusto Lima Diniz
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil.
| | - Willian Giordani
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil.
| | - Zirlane Portugal Costa
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil.
| | - Gabriel R A Margarido
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil.
| | - Juliana Morini K C Perseguini
- Universidade Tecnológica Federal do Paraná, Dois Vizinhos, Paraná 85660-000, Brazil.
- Centro de Recursos Genéticos, Instituto Agronômico de Campinas, Campinas, São Paulo 13075-630, Brazil.
| | - Luciana L Benchimol-Reis
- Centro de Recursos Genéticos, Instituto Agronômico de Campinas, Campinas, São Paulo 13075-630, Brazil.
| | - Alisson F Chiorato
- Centro de Grãos e Fibras, Instituto Agronômico de Campinas, Campinas, São Paulo 13075-630, Brazil.
| | - Antônio Augusto F Garcia
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil.
| | - Maria Lucia Carneiro Vieira
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil.
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19
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Li B, Lu X, Dou J, Aslam A, Gao L, Zhao S, He N, Liu W. Construction of A High-Density Genetic Map and Mapping of Fruit Traits in Watermelon ( Citrullus Lanatus L.) Based on Whole-Genome Resequencing. Int J Mol Sci 2018; 19:ijms19103268. [PMID: 30347873 PMCID: PMC6214002 DOI: 10.3390/ijms19103268] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 10/15/2018] [Accepted: 10/18/2018] [Indexed: 12/26/2022] Open
Abstract
Watermelon (Citrullus lanatus L.) is an important horticultural crop that is grown worldwide and has a high economic value. To dissect the loci associated with important horticultural traits and to analyze the genetic and genomic information of this species, a high-density genetic map was constructed based on whole-genome resequencing (WGR), a powerful high-resolution method for single-nucleotide polymorphism (SNP) marker development, genetic map construction, and gene mapping. Resequencing of both parental lines and 126 recombinant inbred lines (RIL) resulted in the detection of 178,762 single-nucleotide polymorphism (SNP) markers in the parental lines at a sequencing depth greater than four-fold. Additionally, 2132 recombination bin markers comprising 103,029 SNP markers were mapped onto 11 linkage groups (LGs). Substantially more SNP markers were mapped to the genetic map compared with other recent studies. The total length of the linkage map was 1508.94 cM, with an average distance of 0.74 cM between adjacent bin markers. Based on this genetic map, one locus for fruit bitterness, one locus for rind color, and one locus for seed coat color with high LOD scores (58.361, 18.353, 26.852) were identified on chromosome 1, chromosome 8, and chromosome 3, respectively. These prominent loci were identified in a region of 6.16 Mb, 2.07 Mb, and 0.37 Mb, respectively. On the basis of current research, the high-density map and mapping results will provide a valuable tool for identifying candidate genes, map-based gene cloning, comparative mapping, and marker-assisted selection (MAS) in watermelon breeding.
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Affiliation(s)
- Bingbing Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Xuqiang Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Junling Dou
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Ali Aslam
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Lei Gao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Shengjie Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Nan He
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Wenge Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
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Obala J, Saxena RK, Singh VK, Kumar CVS, Saxena KB, Tongoona P, Sibiya J, Varshney RK. Development of sequence-based markers for seed protein content in pigeonpea. Mol Genet Genomics 2018; 294:57-68. [PMID: 30173295 DOI: 10.1007/s00438-018-1484-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 08/22/2018] [Indexed: 12/30/2022]
Abstract
Pigeonpea is an important source of dietary protein to over a billion people globally, but genetic enhancement of seed protein content (SPC) in the crop has received limited attention for a long time. Use of genomics-assisted breeding would facilitate accelerating genetic gain for SPC. However, neither genetic markers nor genes associated with this important trait have been identified in this crop. Therefore, the present study exploited whole genome re-sequencing (WGRS) data of four pigeonpea genotypes (~ 12X coverage) to identify sequence-based markers and associated candidate genes for SPC. By combining a common variant filtering strategy on available WGRS data with knowledge of gene functions in relation to SPC, 108 sequence variants from 57 genes were identified. These genes were assigned to 19 GO molecular function categories with 56% belonging to only two categories. Furthermore, Sanger sequencing confirmed presence of 75.4% of the variants in 37 genes. Out of 30 sequence variants converted into CAPS/dCAPS markers, 17 showed high level of polymorphism between low and high SPC genotypes. Assay of 16 of the polymorphic CAPS/dCAPS markers on an F2 population of the cross ICP 5529 (high SPC) × ICP 11605 (low SPC), resulted in four of the CAPS/dCAPS markers significantly (P < 0.05) co-segregated with SPC. In summary, four markers derived from mutations in four genes will be useful for enhancing/regulating SPC in pigeonpea crop improvement programs.
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Affiliation(s)
- Jimmy Obala
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
- University of KwaZulu-Natal, African Center for Crop Improvement, Scottsville, Pietermaritzburg, 3209, South Africa
| | - Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Vikas K Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - C V Sameer Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - K B Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Pangirayi Tongoona
- University of KwaZulu-Natal, African Center for Crop Improvement, Scottsville, Pietermaritzburg, 3209, South Africa
| | - Julia Sibiya
- University of KwaZulu-Natal, African Center for Crop Improvement, Scottsville, Pietermaritzburg, 3209, South Africa
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India.
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Zhu Z, Li X, Wei Y, Guo S, Sha A. Identification of a Novel QTL for Panicle Length From Wild Rice ( Oryza minuta) by Specific Locus Amplified Fragment Sequencing and High Density Genetic Mapping. FRONTIERS IN PLANT SCIENCE 2018; 9:1492. [PMID: 30459776 PMCID: PMC6232755 DOI: 10.3389/fpls.2018.01492] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 09/25/2018] [Indexed: 05/17/2023]
Abstract
Wild rice possesses a large number of valuable genes that have been lost or do not exist in cultivated rice. To exploit the desirable gene controlling panicle length (PL) in wild rice Oryza minuta, a recombinant inbred line (RIL) population was constructed that was derived from a cross between the long panicle introgression line K1561 with Oryza minuta segments and a short panicle accession G1025. Specific Locus Amplified Fragment (SLAF) sequencing technology was used to uncover single nucleotide polymorphisms (SNPs) and construct the high-density genetic linkage map. Using 201 RIL populations, a high-density genetic map was developed, and spanned 2781.76 cM with an average genetic distance 0.45 cM. The genetic map was composed of 5, 521 markers on 12 chromosomes. Based on this high-density genome map, quantitative trait loci (QTL) for PL were analyzed for 2 years under four environments. Seven QTLs were detected, which were distributed within chromosomes 4, 9, and 10, respectively. pl4.1 was detected twice, and pl10.1 was only detected once. Although pl9.1 was only detected once, it was very near pl9.2 in the genetic map which was detected three times. Thus, we speculate one major QTL exists in the region of pl9.1 and pl9.2 to control PL (temporarily referred to as pl9). pl9 is a potentially novel allele derived from Oryza minuta, and it can be used for genetic improvement of cultivar rice.
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Affiliation(s)
- Zhengzheng Zhu
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
| | - Xiaoqiong Li
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Science, Nanning, China
| | - Yu Wei
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Science, Nanning, China
| | - Sibin Guo
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Science, Nanning, China
- *Correspondence: Sibin Guo, Aihua Sha,
| | - Aihua Sha
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
- *Correspondence: Sibin Guo, Aihua Sha,
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Recent Perspective of Next Generation Sequencing: Applications in Molecular Plant Biology and Crop Improvement. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s40011-016-0770-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Nogué F, Mara K, Collonnier C, Casacuberta JM. Genome engineering and plant breeding: impact on trait discovery and development. PLANT CELL REPORTS 2016; 35:1475-86. [PMID: 27193593 PMCID: PMC4903109 DOI: 10.1007/s00299-016-1993-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/11/2016] [Indexed: 05/03/2023]
Abstract
KEY MESSAGE New tools for the precise modification of crops genes are now available for the engineering of new ideotypes. A future challenge in this emerging field of genome engineering is to develop efficient methods for allele mining. Genome engineering tools are now available in plants, including major crops, to modify in a predictable manner a given gene. These new techniques have a tremendous potential for a spectacular acceleration of the plant breeding process. Here, we discuss how genetic diversity has always been the raw material for breeders and how they have always taken advantage of the best available science to use, and when possible, increase, this genetic diversity. We will present why the advent of these new techniques gives to the breeders extremely powerful tools for crop breeding, but also why this will require the breeders and researchers to characterize the genes underlying this genetic diversity more precisely. Tackling these challenges should permit the engineering of optimized alleles assortments in an unprecedented and controlled way.
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Affiliation(s)
- Fabien Nogué
- INRA AgroParisTech, IJPB, UMR 1318, INRA Centre de Versailles, Route de Saint Cyr, 78026, Versailles Cedex, France.
| | - Kostlend Mara
- INRA AgroParisTech, IJPB, UMR 1318, INRA Centre de Versailles, Route de Saint Cyr, 78026, Versailles Cedex, France
| | - Cécile Collonnier
- INRA AgroParisTech, IJPB, UMR 1318, INRA Centre de Versailles, Route de Saint Cyr, 78026, Versailles Cedex, France
| | - Josep M Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, 08193, Barcelona, Spain
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Yang D, Liu Y, Cheng H, Chang L, Chen J, Chai S, Li M. Genetic dissection of flag leaf morphology in wheat (Triticum aestivum L.) under diverse water regimes. BMC Genet 2016; 17:94. [PMID: 27352616 PMCID: PMC4924301 DOI: 10.1186/s12863-016-0399-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 06/16/2016] [Indexed: 11/10/2022] Open
Abstract
Background Morphological traits related to flag leaves are determinant traits influencing plant architecture and yield potential in wheat (Triticum aestivum L.). However, little is known regarding their genetic controls under drought stress. One hundred and twenty F8-derived recombinant inbred lines from a cross between two common wheat cultivars Longjian 19 and Q9086 were developed to identify quantitative trait loci (QTLs) and to dissect the genetic bases underlying flag leaf width, length, area, length to width ratio and basal angle under drought stress and well-watered conditions consistent over four environments. Results A total of 55 additive and 51 pairs of epistatic QTLs were identified on all 21 chromosomes except 6D, among which additive loci were highly concentrated in a few of same or adjacent marker intervals in individual chromosomes. Two specific marker intervals of Xwmc694-Xwmc156 on chromosome 1B and Xbarc1072-Xwmc272 on chromosome 2B were co-located by additive QTLs for four tested traits. Twenty additive loci were repeatedly detected in more than two environments, suggestive of stable A-QTLs. A majority of QTLs involved significant additive and epistatic effects, as well as QTL × environment interactions (QEIs). Of these, 72.7 % of additive QEIs and 80 % of epistatic QEIs were related to drought stress with significant genetic effects decreasing phenotypic values. By contrast, additive and QEIs effects contributed more phenotypic variation than epistatic effects. Conclusions Flag leaf morphology in wheat was predominantly controlled by additive and QEIs effects, where more QEIs effects occurred in drought stress and depressed phenotypic performances. Several QTL clusters indicated tight linkage or pleiotropy in the inheritance of these traits. Twenty stable QTLs for flag leaf morphology are potentially useful for the genetic improvement of drought tolerance in wheat through QTL pyramiding.
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Affiliation(s)
- Delong Yang
- Gansu Provincial Key Lab of Aridland Crop Science/School of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yuan Liu
- Gansu Provincial Key Lab of Aridland Crop Science/School of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Hongbo Cheng
- Gansu Provincial Key Lab of Aridland Crop Science/School of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Lei Chang
- School of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Jingjing Chen
- Gansu Provincial Key Lab of Aridland Crop Science/School of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Shouxi Chai
- School of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Mengfei Li
- Gansu Provincial Key Lab of Aridland Crop Science/School of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
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25
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Biscarini F, Cozzi P, Casella L, Riccardi P, Vattari A, Orasen G, Perrini R, Tacconi G, Tondelli A, Biselli C, Cattivelli L, Spindel J, McCouch S, Abbruscato P, Valé G, Piffanelli P, Greco R. Genome-Wide Association Study for Traits Related to Plant and Grain Morphology, and Root Architecture in Temperate Rice Accessions. PLoS One 2016; 11:e0155425. [PMID: 27228161 PMCID: PMC4881974 DOI: 10.1371/journal.pone.0155425] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 04/28/2016] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND In this study we carried out a genome-wide association analysis for plant and grain morphology and root architecture in a unique panel of temperate rice accessions adapted to European pedo-climatic conditions. This is the first study to assess the association of selected phenotypic traits to specific genomic regions in the narrow genetic pool of temperate japonica. A set of 391 rice accessions were GBS-genotyped yielding-after data editing-57000 polymorphic and informative SNPS, among which 54% were in genic regions. RESULTS In total, 42 significant genotype-phenotype associations were detected: 21 for plant morphology traits, 11 for grain quality traits, 10 for root architecture traits. The FDR of detected associations ranged from 3 · 10-7 to 0.92 (median: 0.25). In most cases, the significant detected associations co-localised with QTLs and candidate genes controlling the phenotypic variation of single or multiple traits. The most significant associations were those for flag leaf width on chromosome 4 (FDR = 3 · 10-7) and for plant height on chromosome 6 (FDR = 0.011). CONCLUSIONS We demonstrate the effectiveness and resolution of the developed platform for high-throughput phenotyping, genotyping and GWAS in detecting major QTLs for relevant traits in rice. We identified strong associations that may be used for selection in temperate irrigated rice breeding: e.g. associations for flag leaf width, plant height, root volume and length, grain length, grain width and their ratio. Our findings pave the way to successfully exploit the narrow genetic pool of European temperate rice and to pinpoint the most relevant genetic components contributing to the adaptability and high yield of this germplasm. The generated data could be of direct use in genomic-assisted breeding strategies.
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Affiliation(s)
| | | | | | | | | | - Gabriele Orasen
- CREA-Council for Agricultural Research and Economics, Rice Research Unit, 13100 Vercelli, Italy
| | - Rosaria Perrini
- CREA-Council for Agricultural Research and Economics, Rice Research Unit, 13100 Vercelli, Italy
| | - Gianni Tacconi
- CREA-Council for Agricultural Research and Economics, Genomics Research Centre, 29017 Fiorenzuola d’Arda (Piacenza), Italy
| | - Alessandro Tondelli
- CREA-Council for Agricultural Research and Economics, Genomics Research Centre, 29017 Fiorenzuola d’Arda (Piacenza), Italy
| | - Chiara Biselli
- CREA-Council for Agricultural Research and Economics, Rice Research Unit, 13100 Vercelli, Italy
| | - Luigi Cattivelli
- CREA-Council for Agricultural Research and Economics, Genomics Research Centre, 29017 Fiorenzuola d’Arda (Piacenza), Italy
| | - Jennifer Spindel
- Department of Plant Breeding & Genetics, Cornell University, Ithaca, NY, United States of America
| | - Susan McCouch
- Department of Plant Breeding & Genetics, Cornell University, Ithaca, NY, United States of America
| | | | - Giampiero Valé
- CREA-Council for Agricultural Research and Economics, Rice Research Unit, 13100 Vercelli, Italy
- CREA-Council for Agricultural Research and Economics, Genomics Research Centre, 29017 Fiorenzuola d’Arda (Piacenza), Italy
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26
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Valliyodan B, Dan Qiu, Patil G, Zeng P, Huang J, Dai L, Chen C, Li Y, Joshi T, Song L, Vuong TD, Musket TA, Xu D, Shannon JG, Shifeng C, Liu X, Nguyen HT. Landscape of genomic diversity and trait discovery in soybean. Sci Rep 2016; 6:23598. [PMID: 27029319 PMCID: PMC4814817 DOI: 10.1038/srep23598] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 02/18/2016] [Indexed: 02/08/2023] Open
Abstract
Cultivated soybean [Glycine max (L.) Merr.] is a primary source of vegetable oil and protein. We report a landscape analysis of genome-wide genetic variation and an association study of major domestication and agronomic traits in soybean. A total of 106 soybean genomes representing wild, landraces, and elite lines were re-sequenced at an average of 17x depth with a 97.5% coverage. Over 10 million high-quality SNPs were discovered, and 35.34% of these have not been previously reported. Additionally, 159 putative domestication sweeps were identified, which includes 54.34 Mbp (4.9%) and 4,414 genes; 146 regions were involved in artificial selection during domestication. A genome-wide association study of major traits including oil and protein content, salinity, and domestication traits resulted in the discovery of novel alleles. Genomic information from this study provides a valuable resource for understanding soybean genome structure and evolution, and can also facilitate trait dissection leading to sequencing-based molecular breeding.
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Affiliation(s)
- Babu Valliyodan
- Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia 65211, USA
| | - Dan Qiu
- Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia 65211, USA
| | - Gunvant Patil
- Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia 65211, USA
| | - Peng Zeng
- Beijing Genomics Institute-Shenzhen, Shenzhen, 518083, China
| | - Jiaying Huang
- Beijing Genomics Institute-Shenzhen, Shenzhen, 518083, China
| | - Lu Dai
- Beijing Genomics Institute-Shenzhen, Shenzhen, 518083, China
| | - Chengxuan Chen
- Beijing Genomics Institute-Shenzhen, Shenzhen, 518083, China
| | - Yanjun Li
- Beijing Genomics Institute-Shenzhen, Shenzhen, 518083, China
| | - Trupti Joshi
- Department of Molecular Microbiology and Immunology and Medical Research Office, School of Medicine, University of Missouri, Columbia, 65212
- Department of Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, 65211, USA
| | - Li Song
- Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia 65211, USA
| | - Tri D. Vuong
- Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia 65211, USA
| | - Theresa A. Musket
- Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia 65211, USA
| | - Dong Xu
- Department of Molecular Microbiology and Immunology and Medical Research Office, School of Medicine, University of Missouri, Columbia, 65212
| | - J. Grover Shannon
- Division of Plant Sciences and NCSB, University of Missouri-Fisher Delta Research Center, Portageville, MO, 63873, USA
| | - Cheng Shifeng
- Beijing Genomics Institute-Shenzhen, Shenzhen, 518083, China
| | - Xin Liu
- Beijing Genomics Institute-Shenzhen, Shenzhen, 518083, China
| | - Henry T. Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia 65211, USA
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Zhao W, Wang X, Wang H, Tian J, Li B, Chen L, Chao H, Long Y, Xiang J, Gan J, Liang W, Li M. Genome-Wide Identification of QTL for Seed Yield and Yield-Related Traits and Construction of a High-Density Consensus Map for QTL Comparison in Brassica napus. FRONTIERS IN PLANT SCIENCE 2016; 7:17. [PMID: 26858737 PMCID: PMC4729939 DOI: 10.3389/fpls.2016.00017] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 01/08/2016] [Indexed: 05/18/2023]
Abstract
Seed yield (SY) is the most important trait in rapeseed, is determined by multiple seed yield-related traits (SYRTs) and is also easily subject to environmental influence. Many quantitative trait loci (QTLs) for SY and SYRTs have been reported in Brassica napus; however, no studies have focused on seven agronomic traits simultaneously affecting SY. Genome-wide QTL analysis for SY and seven SYRTs in eight environments was conducted in a doubled haploid population containing 348 lines. Totally, 18 and 208 QTLs for SY and SYRTs were observed, respectively, and then these QTLs were integrated into 144 consensus QTLs using a meta-analysis. Three major QTLs for SY were observed, including cqSY-C6-2 and cqSY-C6-3 that were expressed stably in winter cultivation area for 3 years and cqSY-A2-2 only expressed in spring rapeseed area. Trait-by-trait meta-analysis revealed that the 144 consensus QTLs were integrated into 72 pleiotropic unique QTLs. Among them, all the unique QTLs affected SY, except for uq.A6-1, including uq.A2-3, uq.C1-2, uq.C1-3, uq.C6-1, uq.C6-5, and uq.C6-6 could also affect more than two SYRTs. According to the constructed high-density consensus map and QTL comparison from literatures, 36 QTLs from five populations were co-localized with QTLs identified in this study. In addition, 13 orthologous genes were observed, including five each gene for SY and thousand seed weight, and one gene each for biomass yield, branch height, and plant height. The genomic information of these QTLs will be valuable in hybrid cultivar breeding and in analyzing QTL expression in different environments.
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Affiliation(s)
- Weiguo Zhao
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic ImprovementYangling, China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Xiaodong Wang
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural SciencesNanjing, China
| | - Hao Wang
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic ImprovementYangling, China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
- *Correspondence: Hao Wang
| | - Jianhua Tian
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic ImprovementYangling, China
| | - Baojun Li
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic ImprovementYangling, China
| | - Li Chen
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Hongbo Chao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Yan Long
- Institute of Biotechnology, Chinese Academy of Agricultural SciencesBeijing, China
| | - Jun Xiang
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
| | - Jianping Gan
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
| | - Wusheng Liang
- Department of Applied Biological Science, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
- Maoteng Li
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Ali L, Deokar A, Caballo C, Tar'an B, Gil J, Chen W, Millan T, Rubio J. Fine mapping for double podding gene in chickpea. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:77-86. [PMID: 26433827 DOI: 10.1007/s00122-015-2610-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 09/19/2015] [Indexed: 06/05/2023]
Abstract
For the first time, fine mapping for sfl locus was carried out using a battery of new STMS and SNP markers. The target region was delimited to 92.6 Kb where seven annotated genes were found that could be candidate genes for the simple/double podding trait in chickpea. Four recombinant inbred populations (RIP-1, RIP-7, RIP-11, and CPR-01) were used to map the double podding gene (sfl) in chickpea. In RIP-1, the gene was initially mapped on linkage group (LG) 6 between the two sequence-tagged microsatellite site (STMS) markers TA120 and TR1. Eight new STMS markers were added onto LG6 in the target region and sfl locus was finally located between CAGM27819 and CAGM27777 markers within an interval of 2 cM. Seven out of the eight markers were mapped in RIP-7 and its reciprocal RIP-11 confirming the location of the sfl locus to a 4.8 cM interval flanked by TR44 and CAGM27705. Furthermore, using a high-density single nucleotide polymorphism (SNP) map of CPR-01, sfl was mapped to the same genomic region in a 5.1 cM interval between TR44 and the SNP scaffold1646p97220. Five pairs of near isogenic lines (NILs) and eight recombinant inbred lines (RILs) were used to refine this region in the chickpea physical map. Combining data from linkage analysis in four RIPs, marker physical positions and recombination events obtained in both pairs of NILs and selected RILs, sfl could be placed within a genomic window of 92.6 Kb. Seven annotated genes were extracted from this region. The regulator of axillary meristem-predicted gene could be a candidate gene for the simple/double podding gene. This study provides additional set of markers flanking and tightly linked to sfl locus that are useful for marker-assisted selection.
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Affiliation(s)
- L Ali
- Department of Genetics, University of Córdoba, Campus Rabanales Ed. C-5, 14071, Córdoba, Spain
| | - A Deokar
- Crop Development Center, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - C Caballo
- Área de Mejora y Biotecnología, IFAPA, Apdo 3092, 14080, Córdoba, Spain
| | - B Tar'an
- Crop Development Center, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - J Gil
- Department of Genetics, University of Córdoba, Campus Rabanales Ed. C-5, 14071, Córdoba, Spain
| | - W Chen
- Grain Legume Genetics and Physiology Research Unit, USDA-ARS, Washington State University, Pullman, WA, 99164, USA
| | - T Millan
- Department of Genetics, University of Córdoba, Campus Rabanales Ed. C-5, 14071, Córdoba, Spain.
| | - J Rubio
- Área de Mejora y Biotecnología, IFAPA, Apdo 3092, 14080, Córdoba, Spain
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29
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Wang SH, Lim JH, Kim SS, Cho SH, Yoo SC, Koh HJ, Sakuraba Y, Paek NC. Mutation of SPOTTED LEAF3 (SPL3) impairs abscisic acid-responsive signalling and delays leaf senescence in rice. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:7045-59. [PMID: 26276867 PMCID: PMC4765782 DOI: 10.1093/jxb/erv401] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Lesion mimic mutants commonly display spontaneous cell death in pre-senescent green leaves under normal conditions, without pathogen attack. Despite molecular and phenotypic characterization of several lesion mimic mutants, the mechanisms of the spontaneous formation of cell death lesions remain largely unknown. Here, the rice lesion mimic mutant spotted leaf3 (spl3) was examined. When grown under a light/dark cycle, the spl3 mutant appeared similar to wild-type at early developmental stages, but lesions gradually appeared in the mature leaves close to heading stage. By contrast, in spl3 mutants grown under continuous light, severe cell death lesions formed in developing leaves, even at the seedling stage. Histochemical analysis showed that hydrogen peroxide accumulated in the mutant, likely causing the cell death phenotype. By map-based cloning and complementation, it was shown that a 1-bp deletion in the first exon of Oryza sativa Mitogen-Activated Protein Kinase Kinase Kinase1 (OsMAPKKK1)/OsEDR1/OsACDR1 causes the spl3 mutant phenotype. The spl3 mutant was found to be insensitive to abscisic acid (ABA), showing normal root growth in ABA-containing media and delayed leaf yellowing during dark-induced and natural senescence. Expression of ABA signalling-associated genes was also less responsive to ABA treatment in the mutant. Furthermore, the spl3 mutant had lower transcript levels and activities of catalases, which scavenge hydrogen peroxide, probably due to impairment of ABA-responsive signalling. Finally, a possible molecular mechanism of lesion formation in the mature leaves of spl3 mutant is discussed.
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Affiliation(s)
- Seung-Hyun Wang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Jung-Hyun Lim
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Sang-Sook Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Sung-Hwan Cho
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Soo-Cheul Yoo
- Department of Plant Life and Environmental Science, Hankyong National University, Ansung 456-749, Korea
| | - Hee-Jong Koh
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Yasuhito Sakuraba
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Nam-Chon Paek
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang 232-916, Korea
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