Abstract
Spike length (SL) is the key determinant of plant architecture and yield potential. In this study, 193 recombinant inbred lines (RILs) derived from a cross between 13F10 and Chuanmai 42 (CM42) were evaluated for spike length in six environments. Sixty RILs consisting of 30 high and 30 low SLs were genotyped using the bulked segregant analysis exome sequencing (BSE-Seq) analysis for preliminary quantitative trait locus (QTL) mapping. A 6.69 Mb (518.43–525.12 Mb) region on chromosome 5AL was found to have a significant effect on the SL trait. Fifteen competitive allele-specific PCR (KASP) markers were successfully converted from the single nucleotide polymorphisms (SNPs) in the SL target region. Combined with four novel simple sequence repeat (SSR) markers, a genetic linkage map spanning 21.159 cM was constructed. The mapping result confirmed the identity of a major and stable QTL named QSl.cib-5A in the targeted region that explained 7.88–26.60% of the phenotypic variation in SL. QSl.cib-5A was narrowed to a region of 4.84 cM interval corresponding to a 4.67 Mb (516.60–521.27 Mb) physical region in the Chinese Spring RefSeq v2.0 containing 17 high-confidence genes with 25 transcripts. In addition, this QTL exhibited pleiotropic effects on spikelet density (SD), with the phenotypic variances proportion ranging from 11.34 to 19.92%. This study provides a foundational step for cloning the QSl.cib-5A, which is involved in the regulation of spike morphology in common wheat.
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Acknowledgements
We are grateful to Bioacme Biotechnology Co., Ltd. (Wuhan, China, http://www.whbioacme.com) for the technical assistance.
Funding
This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (Precision Seed Design and Breeding, XDA24030402) and Key Project of wheat breeding in Sichuan Province (2021YFYZ0002).
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Guangsi Ji carried out most of the experiments and wrote the manuscript. Tao Wang coordinated the project, conceived and designed experiments. Bo Feng conducted the bioinformatics work, generated and analyzed data, and edited the manuscript. Zhibin Xu, Xiaoli Fan, and Qiang Zhou collected the samples. Qin Yu, Xiaofeng Liu, and Simin Liao performed the laboratory work. All authors read and approved the final manuscript.
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Supplementary Fig. 1 Spike morphology of the parental lines a Spike length of 13F10 (left) and CM42 (right), b Spike density of 13F10 (left) and CM42 (right), The bar represents 1 cm. Supplementary Fig. 2 Phenotype distribution of traits observed in the 13F10×CM42 recombinant inbred line (RIL) population in six environments and BLUE values Traits included spike length (SL), spikelets per spike (SNS), spike density (SD), grain length (GL), grain width (GW), and thousand grain weight (TGW). Environments: Year+Location: SHL (Shuangliu); SHF (Shifang), Supplementary Fig. 3 Distribution and Venn diagram based on SNP and small InDel statistical analyses Distribution of SNP and InDel loci among 21 chromosomes (a), Venn diagram of the SNPs in the four pools (b), Venn diagram of the small InDels in the four pools (c), Supplementary Fig. 4 The results of the Euclidean distance (ED) algorithm, Supplementary Fig. 5 Spike length and spike density of the members of the 13CM population with different alleles in six environments and BLUE data A: lines with the ‘13F10’ allele; B: ‘CM42’ allele. P values were determined using Student’s t test ***P 0.005 ****P 0.001, Supplementary Fig. 6 SNS, TGW, GL and GW of the 13CM population with flanking marker A014150 according to BLUE data BLUE-A: ‘13F10’ allele; BLUE-B: ‘CM42’ allele. P values were determined using the Student’s t test, Supplementary Fig. 7 SNS, TGW, GL and GW of the 13CM population with flanking marker SSR1017719 according to BLUE data BLUE-A: ‘13F10’ allele; BLUE-B: ‘CM42’ allele. P values were determined using the Student’s t test, Supplementary Fig. 8 SL, SD, SNS, TGW, GL and GW of the 13CM population with the Vrn marker according to BLUE data. BLUE-A: ‘13F10’ allele; BLUE-B: ‘CM42’ allele. P values were determined using the Student’s t test. * P 0.05, Supplementary Fig. 9 Sequence alignment of the q/Q gene from 13F10, CM42 and Chinese Spring Only the region spanning the miR172 target site is shown here. (PPTX 2786 KB)
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Ji, G., Xu, Z., Fan, X. et al. Identification of a major and stable QTL on chromosome 5A confers spike length in wheat (Triticum aestivum L.). Mol Breeding 41, 56 (2021). https://doi.org/10.1007/s11032-021-01249-6
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DOI: https://doi.org/10.1007/s11032-021-01249-6