Dynamic analysis of QTLs for green leaf area duration and green leaf number of main stem in wheat

Shi, Yugang; Lian, Y.; Shi, Huawei; Wang, S.G.; Fan, Houbao; Sun, Daizhen; Jing, Ruilian

doi:10.1556/0806.47.2019.06

Cited by 11 publications

(9 citation statements)

References 28 publications

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“…Furthermore, transcription factors (TFs), such as NAC and WRKY families, also play an important role in the regulation of SAGs expression in leaf senescence (Kim et al, 2018 ). Moreover, the genetic basis of senescence in mapping populations and natural populations has been revealed in Arabidopsis thaliana , rice, soybean, maize and wheat (Hebbar et al, 2005 ; Shi et al, 2019 ; Zhao et al, 2019 ; Wang et al, 2020 ; Zhang et al, 2020a ). Recently, a QTL mapping study uncovered the lifespan and senescence patterns in rice using a cross between the Indica and japonica cultivars (Shin et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Uncovering Novel Genomic Regions and Candidate Genes for Senescence-Related Traits by Genome-Wide Association Studies in Upland Cotton (Gossypium hirsutum L.)

Liu

Feng

et al. 2022

Front. Plant Sci.

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Senescence in plants is a complex trait, which is controlled by both genetic and environmental factors and can affect the yield and quality of cotton. However, the genetic basis of cotton senescence remains relatively unknown. In this study, we reported genome-wide association studies (GWAS) based on 185 accessions of upland cotton and 26,999 high-quality single-nucleotide polymorphisms (SNPs) to reveal the genetic basis of cotton senescence. To determine cotton senescence, we evaluated eight traits/indices. Our results revealed a high positive correlation (r>0.5) among SPAD value 20 days after topping (SPAD20d), relative difference of SPAD (RSPAD), nodes above white flower on topping day (NAWF0d), nodes above white flower 7 days after topping (NAWF7d), and number of open bolls on the upper four branches (NB), and genetic analysis revealed that all traits had medium or high heritability ranging from 0.53 to 0.86. Based on a multi-locus method (FASTmrMLM), a total of 63 stable and significant quantitative trait nucleotides (QTNs) were detected, which represented 50 genomic regions (GWAS risk loci) associated with cotton senescence. We observed three reliable loci located on chromosomes A02 (A02_105891088_107196428), D03 (D03_37952328_38393621) and D13 (D13_59408561_60730103) because of their high repeatability. One candidate gene (Ghir_D03G011060) was found in the locus D03_37952328_38393621, and its Arabidopsis thaliana homologous gene (AT5G23040) encodes a cell growth defect factor-like protein (CDF1), which might be involved in chlorophyll synthesis and cell death. Moreover, qRT-PCR showed that the transcript level of Ghir_D03G011060 was down-regulated in old cotton leaves, and virus-induced gene silencing (VIGS) indicated that silencing of Ghir_D03G011060 resulted in leaf chlorosis and promoted leaf senescence. In addition, two candidate genes (Ghir_A02G017660 and Ghir_D13G021720) were identified in loci A02_105891088_107196428 and D13_59408561_60730103, respectively. These results provide new insights into the genetic basis of cotton senescence and will serve as an important reference for the development and implementation of strategies to prevent premature senescence in cotton breeding programs.

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Section: Introductionmentioning

confidence: 99%

Uncovering Novel Genomic Regions and Candidate Genes for Senescence-Related Traits by Genome-Wide Association Studies in Upland Cotton (Gossypium hirsutum L.)

Liu

Feng

et al. 2022

Front. Plant Sci.

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“…These other traits included the following traits: (i) stay green (SG); (ii) flag leaf senescence (FLS); (iii) green leaf area duration (GLAD); (iv) green leaf area of the main stem (GLMS); and (v) black point resistance (BPR). These other traits were found to be associated with spot blotch in several QTL interval studies [22][23][24][25][26][27][28] . The present study is the first study involving MQTL analysis for spot blotch resistance and associated traits for the development of robust markers to be used for MAS.…”

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confidence: 95%

Meta-QTL analysis and identification of candidate genes for multiple-traits associated with spot blotch resistance in bread wheat

Vasistha,

Sharma,

Singh

et al. 2024

Sci Rep

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In bread wheat, a literature search gave 228 QTLs for six traits, including resistance against spot blotch and the following five other related traits: (i) stay green; (ii) flag leaf senescence; (iii) green leaf area duration; (iv) green leaf area of the main stem; and (v) black point resistance. These QTLs were used for metaQTL (MQTL) analysis. For this purpose, a consensus map with 72,788 markers was prepared; 69 of the above 228 QTLs, which were suitable for MQTL analysis, were projected on the consensus map. This exercise resulted in the identification of 16 meta-QTLs (MQTLs) located on 11 chromosomes, with the PVE ranging from 5.4% (MQTL7) to 21.8% (MQTL5), and the confidence intervals ranging from 1.5 to 20.7 cM (except five MQTLs with a range of 36.1–57.8 cM). The number of QTLs associated with individual MQTLs ranged from a maximum of 17 in MQTL3 to 8 each in MQTL5 and MQTL8 and 5 each in MQTL7 and MQTL14. The 16 MQTLs, included 12 multi-trait MQTLs; one of the MQTL also overlapped a genomic region carrying the major spot blotch resistance gene Sb1. Of the total 16 MQTLs, 12 MQTLs were also validated through marker-trait associations that were available from earlier genome-wide association studies. The genomic regions associated with MQTLs were also used for the identification of candidate genes (CGs) and led to the identification of 516 CGs encoding 508 proteins; 411 of these proteins are known to be associated with resistance against several biotic stresses. In silico expression analysis of CGs using transcriptome data allowed the identification of 71 differentially expressed CGs, which were examined for further possible studies. The findings of the present study should facilitate fine-mapping and cloning of genes, enabling Marker Assisted Selection.

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“…Elimination of heterozygosity simplifies genome sequencing, reverse breeding, quantitative genetic research and discovering of recessive, dominant and deleterious mutations. That's why DHs are interesting objects of studies in many research areas including physiology, molecular biology, genetics and epigenetics (Maluszynski et al, 1996;Castillo et al, 2001;Touraev et al, 2001;Forster et al, 2007;Szarejko and Forster, 2007 and references therein;Dirks et al, 2009;Dunwell, 2010;Chauhan and Khurana, 2011;Ferrie and Möllers, 2011;Krzewska et al, 2012Krzewska et al, , 2017Marathi et al, 2012;Żur et al, 2014a,b, 2015aBarakat et al, 2017;Ren et al, 2017;Song et al, 2017;Shchukina et al, 2018;Tyrka et al, 2018;Nowicka et al, 2019;Shi et al, 2019;Testillano, 2019;Wajdzik et al, 2019;Bilichak et al, 2020;Malaga et al, 2020). Furthermore, DH technology combined with marker assisted selection (MAS) enables precise identification of plants with enhanced/silenced expression of even one gene of interest within the genome.…”

Section: Introductionmentioning

confidence: 99%

Proteins, Small Peptides and Other Signaling Molecules Identified as Inconspicuous but Possibly Important Players in Microspores Reprogramming Toward Embryogenesis

Dubas¹,

Żur²,

Moravčíková³

et al. 2021

Front. Sustain. Food Syst.

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In this review, we describe and integrate the latest knowledge on the signaling role of proteins and peptides in the stress-induced microspore embryogenesis (ME) in some crop plants with agricultural importance (i.e., oilseed rape, tobacco, barley, wheat, rice, triticale, rye). Based on the results received from the most advanced omix analyses, we have selected some inconspicuous but possibly important players in microspores reprogramming toward embryogenic development. We provide an overview of the roles and downstream effect of stress-related proteins (e.g., β-1,3-glucanases, chitinases) and small signaling peptides, especially cysteine—(e.g., glutathione, γ-thionins, rapid alkalinization factor, lipid transfer, phytosulfokine) and glycine-rich peptides and other proteins (e.g., fasciclin-like arabinogalactan protein) on acclimation ability of microspores and the cell wall reconstruction in a context of ME induction and haploids/doubled haploids (DHs) production. Application of these molecules, stimulating the induction and proper development of embryo-like structures and green plant regeneration, brings significant improvement of the effectiveness of DHs procedures and could result in its wider incorporation on a commercial scale. Recent advances in the design and construction of synthetic peptides–mainly cysteine-rich peptides and their derivatives–have accelerated the development of new DNA-free genome-editing techniques. These new systems are evolving incredibly fast and soon will find application in many areas of plant science and breeding.

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Dynamic analysis of QTLs for green leaf area duration and green leaf number of main stem in wheat

Cited by 11 publications

References 28 publications

Uncovering Novel Genomic Regions and Candidate Genes for Senescence-Related Traits by Genome-Wide Association Studies in Upland Cotton (Gossypium hirsutum L.)

Uncovering Novel Genomic Regions and Candidate Genes for Senescence-Related Traits by Genome-Wide Association Studies in Upland Cotton (Gossypium hirsutum L.)

Meta-QTL analysis and identification of candidate genes for multiple-traits associated with spot blotch resistance in bread wheat

Proteins, Small Peptides and Other Signaling Molecules Identified as Inconspicuous but Possibly Important Players in Microspores Reprogramming Toward Embryogenesis

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