Mapping QTL for leaf pigment content at dynamic development stage and analyzing Meta-QTL in rice

Li, Lamei; Peng, Youlin; Tang, Shiwen; Yu, Dunji; Tian, Min; Guo, Faping; Chen, Yongjun; Yang, Guotao; Wang, Xuechun; Hu, Yungao

doi:10.1007/s10681-021-02820-0

Cited by 4 publications

(2 citation statements)

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“…Meta-QTL analysis is a powerful approach to identify stable and large-effect QTLs and then to refine their position by integrating the QTL mapping results in multiple studies. Meta-QTL studies have been conducted in several major crops for various traits, such as leaf pigment content in rice [ 21 ], root traits in maize [ 22 ], grain yield and associated traits in wheat [ 23 ], and iron and zinc concentration and content in the seeds of common bean [ 24 ]. In melon, the large number of QTL mapping results related to the same trait makes it possible to perform meta-QTL analysis to confirm and narrow down the QTL mapping intervals.…”

Section: Introductionmentioning

confidence: 99%

Telomere-to-telomere genome assembly of melon (Cucumis melo L. var. inodorus) provides a high-quality reference for meta-QTL analysis of important traits

Wei,

Huang,

et al. 2023

Horticulture Research

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Melon is an important vegetable crop with extensive diversity in many horticultural groups. To explore the genomic diversity, it is needed to assemble more high-quality complete genomes from different melon accessions. Meanwhile, a large number of QTLs have been mapped in several researches. Integration of the published QTLs onto a complete genome can provide more accurate information for candidate gene cloning. To address these problems, a telomere-to-telomere (T2T) genome of the elite melon landrace Kuizilikjiz (Cucumis melo L. var. inodorous) was de novo assembled and all the published QTLs were projected onto it in this study. The results showed a high-quality Kuizilikjiz genome with the size of 379.2 Mb and N50 of 31.7 Mb was de novo assembled using the combination of short-reads, PacBio high-fidelity long reads, Hi-C data, and a high-density genetic map. Each chromosome contained the centromere and telomeres at both ends. A large number of structural variations were observed between Kuizilikjiz and the other published genomes. A total of 1,294 QTLs published in 67 studies were collected and projected onto the T2T genome. Several clustered, co-localized, and overlapped QTLs were determined. Furthermore, the 20 stable meta-QTLs were identified, which significantly reduced the mapping intervals of the initial QTLs and greatly facilitated identification of the candidate genes. Collectively, the T2T genome assembly together with the numerous projected QTLs will not only broaden the high-quality genome resources but also provide valuable and abundant QTL information for cloning the genes controlling important traits in melon.

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Section: Introductionmentioning

confidence: 99%

Telomere-to-telomere genome assembly of melon (Cucumis melo L. var. inodorus) provides a high-quality reference for meta-QTL analysis of important traits

Wei,

Huang,

et al. 2023

Horticulture Research

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“…In wheat, MQTL analysis has also been successfully used to identify consensus QTL regions for yield-related traits [35][36][37][38], drought and heat tolerance [39][40][41][42], disease resistance [43][44][45][46], grain quality traits [31,[47][48][49], root-related traits [50][51][52], and so on. Likewise, MQTL has also been widely used for the different quantitative traits in different species such as rice (Oryza sativa L.) [53][54][55], maize (Zea mays L.) [56][57][58], barley (Hordeum vulgare L.) [59], and cotton (Gossypium hirsutum L.) [60]. MQTL analysis examined relevant QTL studies and refined the confidence intervals (CIs) of QTLs or QTL clusters to identify more reliable QTLs [38].…”

Section: Introductionmentioning

confidence: 99%

Deciphering key genomic regions controlling flag leaf size in wheat via integration of meta-QTL and in silico transcriptome assessment

Kong

Zhang³

et al. 2023

BMC Genomics

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Background Grain yield is a complex and polygenic trait influenced by the photosynthetic source-sink relationship in wheat. The top three leaves, especially the flag leaf, are considered the major sources of photo-assimilates accumulated in the grain. Determination of significant genomic regions and candidate genes affecting flag leaf size can be used in breeding for grain yield improvement. Results With the final purpose of understanding key genomic regions for flag leaf size, a meta-analysis of 521 initial quantitative trait loci (QTLs) from 31 independent QTL mapping studies over the past decades was performed, where 333 loci eventually were refined into 64 meta-QTLs (MQTLs). The average confidence interval (CI) of these MQTLs was 5.28 times less than that of the initial QTLs. Thirty-three MQTLs overlapped the marker trait associations (MTAs) previously reported in genome-wide association studies (GWAS) for flag leaf traits in wheat. A total of 2262 candidate genes for flag leaf size, which were involved in the peroxisome, basal transcription factor, and tyrosine metabolism pathways were identified in MQTL regions by the in silico transcriptome assessment. Of these, the expression analysis of the available genes revealed that 134 genes with > 2 transcripts per million (TPM) were highly and specifically expressed in the leaf. These candidate genes could be critical to affect flag leaf size in wheat. Conclusions The findings will make further insight into the genetic determinants of flag leaf size and provide some reliable MQTLs and putative candidate genes for the genetic improvement of flag leaf size in wheat.

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Meta-analysis of Mapping Studies: Integrating QTLs Towards Candidate Gene Discovery

Kumari,

Sharma,

Sahil

et al. 2024

Springer Protocols Handbooks

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Mapping QTL for leaf pigment content at dynamic development stage and analyzing Meta-QTL in rice

Cited by 4 publications

References 66 publications

Telomere-to-telomere genome assembly of melon (Cucumis melo L. var. inodorus) provides a high-quality reference for meta-QTL analysis of important traits

Telomere-to-telomere genome assembly of melon (Cucumis melo L. var. inodorus) provides a high-quality reference for meta-QTL analysis of important traits

Deciphering key genomic regions controlling flag leaf size in wheat via integration of meta-QTL and in silico transcriptome assessment

Meta-analysis of Mapping Studies: Integrating QTLs Towards Candidate Gene Discovery

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