HpQTL: a geometric morphometric platform to compute the genetic architecture of heterophylly

Sun, Lidan; Wang, Jing; Zhu, Xuli; Jiang, Libo; Gosik, Kirk; Sang, Mengmeng; Sun, Fangzhou; Cheng, Tangren; Zhang, Qixiang; Wu, Rongling

doi:10.1093/bib/bbx011

Cited by 8 publications

(6 citation statements)

References 35 publications

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“…However, the above models for shape mapping cannot be used to characterize heterophylly variation, and these methods neglect the differentiation of leaf shape at multiple positions within the same plant. To resolve this problem, the principle of GM-based shape mapping was expanded to map QTLs for the shapes of leaves in various positions, and this method can test specific QTLs potentially mediating heterophyllous variation throughout the genome ( Sun et al, 2018 ). These shape mapping tools are valuable for exploring the genetic architecture of heterophylly.…”

Section: Introductionmentioning

confidence: 99%

Genetic Architecture of Heterophylly: Single and Multi-Leaf Genome-Wide Association Mapping in Populus euphratica

et al. 2022

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Heterophylly is an adaptive strategy used by some plants in response to environmental changes. Due to the lack of representative plants with typical heteromorphic leaves, little is known about the genetic architecture of heterophylly in plants and the genes underlying its control. Here, we investigated the genetic characteristics underlying changes in leaf shape based on the model species, Populus euphratica, which exhibits typical heterophylly. A set of 401,571 single-nucleotide polymorphisms (SNPs) derived from whole-genome sequencing of 860 genotypes were associated with nine leaf traits, which were related to descriptive and shape data using single- and multi-leaf genome-wide association studies (GWAS). Multi-leaf GWAS allows for a more comprehensive understanding of the genetic architecture of heterophylly by considering multiple leaves simultaneously. The single-leaf GWAS detected 140 significant SNPs, whereas the multi-leaf GWAS detected 200 SNP-trait associations. Markers were found across 19 chromosomes, and 21 unique genes were implicated in traits and serve as potential targets for selection. Our results provide novel insights into the genomic architecture of heterophylly, and provide candidate genes for breeding or engineering P. euphratica. Our observations also improve understanding of the intrinsic mechanisms of plant growth, evolution, and adaptation in response to climate change.

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Section: Introductionmentioning

confidence: 99%

Genetic Architecture of Heterophylly: Single and Multi-Leaf Genome-Wide Association Mapping in Populus euphratica

et al. 2022

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“…The marriage of GM and functional mapping has begun to move beyond the conceptual stage and been shown to facilitate the identification of QTLs responsible for heterophylly (Sun et al. , 2018).…”

Section: Introductionmentioning

confidence: 99%

Long‐read genome assembly and genetic architecture of fruit shape in the bottle gourd

Wang

Sun

et al. 2021

The Plant Journal

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SUMMARY The bottle gourd (Lagenaria siceraria, Cucurbitaceae) is an important horticultural crop exhibiting tremendous diversity in fruit shape. The genetic architecture of fruit shape variation in this species remains unknown. We assembled a long‐read‐based, high‐quality reference genome (ZAAS_Lsic_2.0) with a contig N50 value over 390‐fold greater than the existing reference genomes. We then focused on dissection of fruit shape using a one‐step geometric morphometrics‐based functional mapping approach. We identified 11 quantitative trait loci (QTLs) responsible for fruit shape (fsQTLs), reconstructed their visible effects and revealed syntenic relationships of bottle gourd fsQTLs with 12 fsQTLs previously reported in cucumber, melon or watermelon. Homologs of several well‐known and newly identified fruit shape genes, including SUN, OFP, AP2 and auxin transporters, were comapped with bottle gourd QTLs.

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“…Genome-wide association study (GWAS) methods can be applied for highly accurate mapping of trait-associated loci, to elucidate the genetic architecture of heterophylly. In this process, heterophylly is quantitatively defined as a multivariate phenotype (e.g., in terms of length, width, and the length/width ratio along the shoot axis) or precisely measured using geometric morphometrics, e.g., multiple radius centroid contour (RCC) curves of outline coordinates along the leaf margin (Fu et al, 2018;Sun et al, 2018). Functional mapping techniques facilitate the study of genetic control over trait formation using dynamic models that integrate the pathways underlying phenotypic formation (Ma et al, 2002;Sun and Wu, 2015).…”

Section: Introductionmentioning

confidence: 99%

Heterophylly Quantitative Trait Loci Respond to Salt Stress in the Desert Tree Populus euphratica

et al. 2021

Front. Plant Sci.

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Heterophylly, or leaf morphological changes along plant shoot axes, is an important indicator of plant eco-adaptation to heterogeneous microenvironments. Despite extensive studies on the genetic control of leaf shape, the genetic architecture of heterophylly remains elusive. To identify genes related to heterophylly and their associations with plant saline tolerance, we conducted a leaf shape mapping experiment using leaves from a natural population of Populus euphratica. We included 106 genotypes grown under salt stress and salt-free (control) conditions using clonal seedling replicates. We developed a shape tracking method to monitor and analyze the leaf shape using principal component (PC) analysis. PC1 explained 42.18% of the shape variation, indicating that shape variation is mainly determined by the leaf length. Using leaf length along shoot axes as a dynamic trait, we implemented a functional mapping-assisted genome-wide association study (GWAS) for heterophylly. We identified 171 and 134 significant quantitative trait loci (QTLs) in control and stressed plants, respectively, which were annotated as candidate genes for stress resistance, auxin, shape, and disease resistance. Functions of the stress resistance genes ABSCISIC ACIS-INSENSITIVE 5-like (ABI5), WRKY72, and MAPK3 were found to be related to many tolerance responses. The detection of AUXIN RESPONSE FACTOR17-LIKE (ARF17) suggests a balance between auxin-regulated leaf growth and stress resistance within the genome, which led to the development of heterophylly via evolution. Differentially expressed genes between control and stressed plants included several factors with similar functions affecting stress-mediated heterophylly, such as the stress-related genes ABC transporter C family member 2 (ABCC2) and ABC transporter F family member (ABCF), and the stomata-regulating and reactive oxygen species (ROS) signaling gene RESPIRATORY BURST OXIDASE HOMOLOG (RBOH). A comparison of the genetic architecture of control and salt-stressed plants revealed a potential link between heterophylly and saline tolerance in P. euphratica, which will provide new avenues for research on saline resistance-related genetic mechanisms.

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HpQTL: a geometric morphometric platform to compute the genetic architecture of heterophylly

Cited by 8 publications

References 35 publications

Genetic Architecture of Heterophylly: Single and Multi-Leaf Genome-Wide Association Mapping in Populus euphratica

Genetic Architecture of Heterophylly: Single and Multi-Leaf Genome-Wide Association Mapping in Populus euphratica

Long‐read genome assembly and genetic architecture of fruit shape in the bottle gourd

Heterophylly Quantitative Trait Loci Respond to Salt Stress in the Desert Tree Populus euphratica

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