Abstract
Key message
The fiber length-related qFL-A12-5 identified in CSSLs introgressed from Gossypium barbadense into Gossypium hirsutum was fine-mapped to an 18.8 kb region on chromosome A12, leading to the identification of the GhTPR gene as a potential regulator of cotton fiber length.
Abstract
Fiber length is a key determinant of fiber quality in cotton, and it is a key target of artificial selection for breeding and domestication. Although many fiber length-related quantitative trait loci have been identified, there are few reports on their fine mapping or candidate gene validation, thus hampering efforts to understand the mechanistic basis of cotton fiber development. Our previous study identified the qFL-A12-5 associated with superior fiber quality on chromosome A12 in the chromosome segment substitution line (CSSL) MBI7747 (BC4F3:5). A single segment substitution line (CSSL-106) screened from BC6F2 was backcrossed to construct a larger segregation population with its recurrent parent CCRI45, thus enabling the fine mapping of 2852 BC7F2 individuals using denser simple sequence repeat markers to narrow the qFL-A12-5 to an 18.8 kb region of the genome, in which six annotated genes were identified in Gossypium hirsutum. Quantitative real-time PCR and comparative analyses led to the identification of GH_A12G2192 (GhTPR) encoding a tetratricopeptide repeat-like superfamily protein as a promising candidate gene for qFL-A12-5. A comparative analysis of the protein-coding regions of GhTPR among Hai1, MBI7747, and CCRI45 revealed two non-synonymous mutations. The overexpression of GhTPR resulted in longer roots in Arabidopsis, suggesting that GhTPR may regulate cotton fiber development. These results provide a foundation for future efforts to improve cotton fiber length.
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Data availability
The datasets generated during and/or analyzed during the current study are available from the corresponding author upon reasonable request.
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Funding
This study was funded by the National Natural Science Foundation of China (32272188, 32070560), the Natural Science Foundation of Henan Province (202300410549), China Agriculture Research System of MOF and MARA, Hainan Yazhou Bay Seed Lab (B21HJ0210), the National Agricultural Science and Technology Innovation Project for CAAS (CAAS-ASTIP-2016-ICR), the Xinjiang Production and Construction Corps Innovation Program for Science and Technology Talents (2020CB005), and the National Key R&D Program for Crop Breeding (2016YFD0100306).
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YY, QL, and YS conceived and designed the experiments. XX, PL, ZL, WG, AL, QG, XD, YP, and SL carried out the assessment of lint percentage. XX, RL, and JG conducted the experiment. XX, QC, HZ, RP, YP, HS, and JP revised the language and manuscript. XX wrote the manuscript. All authors have read and approved the final version of the manuscript.
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Figure S1
Program for developing the mapping population. (TIF 463 kb)
Figure S2
Frequency distribution for fiber length, fiber uniformity, fiber micronaire, fiber strength, bell weight, and lint of the primary mapping population BC6F2 (TIF 2445 kb)
Figure S3
Frequency distributions for fiber length, fiber uniformity, fiber strength, and fiber micronaire of the primary mapping population BC6F2:3. (a) Frequency distribution of the primary BC6F2:3 population in Anyang, Henan in 2017. (b) Frequency distribution of the primary BC6F2:3 population in Korla, Xinjiang, in 2017 (TIF 1813 kb)
Figure S4
Frequency distribution for fiber length, fiber uniformity, fiber strength, fiber micronaire, bell weight, and lint of the fine-mapped BC7F2 population (TIF 2375 kb)
Figure S5
Frequency distribution for fiber length, fiber uniformity, fiber strength, fiber micronaire, bell weight, and lint of the fine-mapped BC7F2:3 population (TIF 2407 kb)
Figure S6
Chromosomal locations of QTLs of qFL-A12-5 in the primary mapping population BC6F2. NOTE: The genetic map on the left of the chromosomes indicates the genetic distance (cM) (TIF 134 kb)
Figure S7
The ~2 kb genome sequences in the upstream region of GhTPR in Hai 1, MBI774, CCRI45, and TM-1 (TIF 613 kb)
Figure S8
The Cis-acting regulatory elements (CARE) analyses in the GhTPR promoter region in Hai1 (TIF 172 kb)
Figure S9
Epidermal hairs on the stem of transgenic Arabidopsis plants overexpressing GhTPR under the Cauliflower mosaic virus (CaMV) 35S promoter. (a) Comparison of the epidermal hairs on the stem between the transgenic lines and the wild type. (b) Analysis of the number of epidermal hairs on the stem between the transgenic lines and the wild type. (c) Expression level of the GhTPR gene in the stems of the transgenic lines (TIF 7942 kb)
Table S1
Phenotypic analysis of fiber quality and yield traits in the primary populations of BC6F2 and BC6F2:3 (DOCX 21 kb)
Table S2
Correlation coefficients corresponding to fiber length (FL) traits in the mapping populations (DOCX 15 kb)
Table S3
ANOVA analysis for fiber length (FL) traits in the mapping populations (DOCX 16 kb)
Table S4
qRT-PCR primers for candidate genes in the qFL-A12-5 interval were developed from the G. hirsutum genome sequence (DOCX 16 kb)
Table S5
Clone primers for candidate genes in the qFL-A12-5 interval were developed from the G. hirsutum genome sequence (DOCX 16 kb)
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Xiao, X., Liu, R., Gong, J. et al. Fine mapping and candidate gene analysis of qFL-A12-5: a fiber length-related QTL introgressed from Gossypium barbadense into Gossypium hirsutum. Theor Appl Genet 136, 48 (2023). https://doi.org/10.1007/s00122-023-04247-8
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DOI: https://doi.org/10.1007/s00122-023-04247-8