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QTL mapping and validation of bread wheat flag leaf morphology across multiple environments in different genetic backgrounds

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Abstract

Key message

Eight major and stably expressed QTL for flag leaf morphology across eleven environments were identified and validated using newly developed KASP markers in seven biparental populations with different genetic backgrounds.

Abstract

Flag leaf morphology is a determinant trait influencing plant architecture and yield potential in wheat (Triticum aestivum L.). A recombinant inbred line (RIL) population with a 55 K SNP-based constructed genetic map was used to map quantitative trait loci (QTL) for flag leaf length (FLL), width (FLW), area (FLA), angle (FLANG), opening angle (FLOA), and bend angle (FLBA) in eleven environments. Eight major QTL were detected in 11 environments with 5.73–54.38% of explained phenotypic variation. These QTL were successfully verified using the newly developed Kompetitive Allele Specific PCR (KASP) markers in six biparental populations with different genetic backgrounds. Among these 8 major QTL, two co-located intervals were identified. Significant interactions for both FLL- and FLW-related QTL were detected. Comparison analysis showed that QFll.sau-SY-2B and QFla.sau-SY-2B are likely new loci. Significant relationships between flag leaf- and yield-related traits were observed and discussed. Several genes associated with leaf development including the ortholog of maize ZmRAVL1, a B3-domain transcription factor involved in regulation of leaf angle, were predicted in physical intervals harboring these major QTL on reference genomes of bread wheat ‘Chinese spring’, T. turgidum, and Aegilops tauschii. Taken together, these results broaden our understanding on genetic basis of flag leaf morphology and provide clues for fine mapping and marker-assisted breeding wheat with optimized plant architecture for promising loci.

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Acknowledgements

This work is supported by the National Natural Science Foundation of China (31970243 and 31971937), the Key Research and Development Program of Sichuan Province (2018NZDZX0002), the Applied Basic Research Programs of Science and Technology Department of Sichuan Province (2020YJ0140), and the Key Projects of Scientific and Technological Activities for Overseas Students of Sichuan Province. We thank the anonymous referees for critical reading and revising this manuscript.

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  1. Yang Tu and Hang Liu have contributed equally to this paper.

Authors and Affiliations

  1. State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China

    Yang Tu, Hang Liu, Jiajun Liu, Huaping Tang, Yang Mu, Mei Deng, Qiantao Jiang, Yaxi Liu, Guoyue Chen, Jirui Wang, Pengfei Qi, Yuanying Peng, Yunfeng Jiang, Qiang Xu, Houyang Kang, Xiujin Lan, Yuming Wei, Youliang Zheng & Jian Ma

  2. College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China

    Zhien Pu

  3. College of Resources, Sichuan Agricultural University, Chengdu, 611130, China

    Guangdeng Chen

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Contributions

YT and HL performed the entire study and drafted this manuscript. JJL did phenotype measurement and data analysis. HPT and YM did field work and data analysis. MD, QTJ, and YXL helped with data collection and analysis. GYC, JRW, PFQ, ZEP, and GDC did QTL analysis and manuscript revision. YYP and YFJ developed genetic populations. HYK and XJL discussed results and revised the manuscript. YMW and YLZ guided the study and revised the manuscript. JM designed the experiments, guided the entire study, participated in data analysis, and wrote and extensively revised this manuscript. All authors participated in the research and approved the final manuscript.

Corresponding author

Correspondence to Jian Ma.

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All experiments and data analyses were conducted in Sichuan. All authors contributed to the study and approved the final version for submission. The manuscript has not been submitted to any other journal.

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122_2020_3695_MOESM1_ESM.xlsx

Table S1 The ecological points where flag leaf length (FLL), flag leaf width (FLW), flag leaf area (FLA), flag leaf angle (FLANG), flag leaf opening angle (FLOA), flag leaf bend angle (FLBA), spikelet number per spike (SNS), grain length (GL), grain width (GW) and thousand-grain weight (TGW) were measured. (XLSX 13 kb)

Table S2 The primer sequences and PCR program of candidate genes (XLSX 10 kb)

Table S3 Correlation coefficients of flag leaf-related traits in different environments (XLSX 12 kb)

122_2020_3695_MOESM4_ESM.xlsx

Table S4 Minor quantitative trait loci (QTL) for flag leaf-related traits were detected in all the environments in the 20828 / SY95-71 (2SY) population. (XLSX 19 kb)

Table S5 Details of KASP markers used for validation of QTL in six populations (XLSX 12 kb)

122_2020_3695_MOESM6_ESM.xlsx

Table S6 Comparison of the major quantitative trait loci (QTL) identified in this study with those reported previously for flag leaf-related traits (XLSX 14 kb)

Table S7 The sequences of flanking markers Xedm97.1 and Xwmc317 for QFll-2B (XLSX 10 kb)

122_2020_3695_MOESM8_ESM.xlsx

Table S8 The differences of minor quantitative trait loci (QTL) for flag leaf-related traits detected between the 20828 / SY95-71 (2SY) and 20828 / CN16 (2CN) population (XLSX 35 kb)

122_2020_3695_MOESM9_ESM.xlsx

Table S9 Quantitative trait loci (QTL) for spikelet number per spike (SNS), grain length (GL), grain width (GW), thousand-grain weight (TGW), flag leaf width (FLW), flag leaf opening angle(FLOA) and flag leaf bend angle(FLBA) were detected using BLUP data in the 20828 / SY95-71 (2SY) (XLSX 9 kb)

Table S10 Predicated genes in the interval of the major QTL (XLSX 68 kb)

122_2020_3695_MOESM11_ESM.tiff

Fig. S1 Frequency distributions of flag leaf-related traits (FLL, flag leaf length; FLW, flag leaf width; FLA, flag leaf area; FLANG, flag leaf angle; FLOA, flag-leaf opening angle; FLBA, flag-leaf bend angle) in the 2SY population evaluated across ten environments. (TIFF 1585 kb)

122_2020_3695_MOESM12_ESM.tiff

Fig. S2 The effects of two major quantitative trait loci (QTL) on target traits of the 20828 / SY95-71 (2SY) population. a The effects of QFll.sau-SY-2B and QFll.sau-SY-5B on FLL; b The effects of QFlw.sau-SY-2B and QFlw.sau-SY-2D on FLW; + and - represent lines with and without the positive alleles of the target QTL based on the flanking markers the corresponding QTL, respectively. Different lowercase letters indicate significant differences at 0.01 level. Difference value between a given groups was indicated above the line. (TIFF 164 kb)

122_2020_3695_MOESM13_ESM.tiff

Fig. S3 The effects of eight major quantitative trait loci (QTL) on yield related traits of the 20828 / SY95-71 (2SY) population. a The effects of QFll.sau-SY-2B and QFll.sau-SY-5B on GW, GL, TGW and SNS; b the effects of QFlw.sau-SY-2B and QFlw.sau-SY-2D on GW, GL, TGW and SNS; c the effects of QFlang.sau-SY-4B on GW, GL, TGW and SNS; d the effects of QFloa.sau-SY-6D/ QFlba.sau-SY-6D on GW, GL, TGW and SNS. + and - represent lines with and without the positive alleles of the target QTL based on the flanking markers the corresponding QTL, respectively. **Significant at P = 0.01. *Significant at P = 0.05. Difference value between a given groups was indicated above the line. (TIFF 339 kb)

122_2020_3695_MOESM14_ESM.tiff

Fig. S4 The flank marker Xedm97.1 of QFll-2B detected polymorphism in 20828 / SY95-71 (2SY) population. a Alleles of these lines were derived from parent 20828; b alleles of these lines were derived from parent SY95-71. (TIFF 2784 kb)

Fig. S5 The expression patterns of candidate genes (TIFF 444 kb)

Fig. S6 The gene sequence of TraesCS2B01G457600 (TIFF 1312 kb)

Fig. S7 The gene sequence of TraesCS2B01G458800 (TIFF 1252 kb)

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Tu, Y., Liu, H., Liu, J. et al. QTL mapping and validation of bread wheat flag leaf morphology across multiple environments in different genetic backgrounds. Theor Appl Genet 134, 261–278 (2021). https://doi.org/10.1007/s00122-020-03695-w

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  • DOI: https://doi.org/10.1007/s00122-020-03695-w

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