Genomic structural equation modelling provides a whole-system approach for the future crop breeding

He, Tengbing; Angessa, Tefera Tolera; Hill, Camilla Beate; Zhang, Xiaoqi; Chen, Kefei; Luo, Hao; Wang, Yonggang; Karunarathne, Sakura D; Zhou, Gaofeng; Tan, Cong; Wang, Penghao; Westcott, Sharon; Li, Chengdao

doi:10.1007/s00122-021-03865-4

Cited by 5 publications

(2 citation statements)

References 54 publications

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“…The effect of each SNP on each trait was estimated within a genomic SEM framework [ 31 ]. The estimate of the SNP effect and model test followed the steps as described in [ 48 ] and was implemented with GenomicSEM [ 31 ]. Experimental data are currently not compatible with the hypothesis that every mutation (or gene) affects every trait [ 49 ].…”

Section: Methodsmentioning

confidence: 99%

Pleiotropy Structures Plant Height and Seed Weight Scaling in Barley despite Long History of Domestication and Breeding Selection

Angessa

2023

Plant Phenomics

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Size scaling describes the relative growth rates of different body parts of an organism following a positive correlation. Domestication and crop breeding often target the scaling traits in the opposite directions. The genetic mechanism of the size scaling influencing the pattern of size scaling remains unexplored. Here, we revisited a diverse barley ( Hordeum vulgare L.) panel with genome-wide single-nucleotide polymorphisms (SNPs) profile and the measurement of their plant height and seed weight to explore the possible genetic mechanisms that may lead to a correlation of the two traits and the influence of domestication and breeding selection on the size scaling. Plant height and seed weight are heritable and remain positively correlated in domesticated barley regardless of growth type and habit. Genomic structural equation modeling systematically evaluated the pleiotropic effect of individual SNP on the plant height and seed weight within a trait correlation network. We discovered seventeen novel SNPs (quantitative trait locus) conferring pleiotropic effect on plant height and seed weight, involving genes with function in diverse traits related to plant growth and development. Linkage disequilibrium decay analysis revealed that a considerable proportion of genetic markers associated with either plant height or seed weight are closely linked in the chromosome. We conclude that pleiotropy and genetic linkage likely form the genetic bases of plant height and seed weight scaling in barley. Our findings contribute to understanding the heritability and genetic basis of size scaling and open a new venue for seeking the underlying mechanism of allometric scaling in plants.

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Section: Methodsmentioning

confidence: 99%

Pleiotropy Structures Plant Height and Seed Weight Scaling in Barley despite Long History of Domestication and Breeding Selection

Angessa

2023

Plant Phenomics

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“…GA also regulates flowering in cereal crops (King and Evans, 2003). Reduced GA signals delay flowering (Boden et al ., 2014), which can negatively impact yield (He et al ., 2021). As climate change affects the intensity and frequency of precipitation, there is an urgent need for plant breeders to select short‐statured barley cultivars with enhanced early emergence characteristics.…”

Section: Introductionmentioning

confidence: 99%

New semi‐dwarfing alleles with increased coleoptile length by gene editing of gibberellin 3‐oxidase 1 using CRISPR‐Cas9 in barley (Hordeum vulgare L.)

Cheng

Hill

Han

et al. 2023

Plant Biotechnology Journal

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Summary The green revolution was based on genetic modification of the gibberellin (GA) hormone system with “dwarfing” gene mutations that reduces GA signals, conferring shorter stature, thus enabling plant adaptation to modern farming conditions. Strong GA‐related mutants with shorter stature often have reduced coleoptile length, discounting yield gain due to their unsatisfactory seedling emergence under drought conditions. Here we present gibberellin (GA) 3‐oxidase1 (GA3ox1) as an alternative semi‐dwarfing gene in barley that combines an optimal reduction in plant height without restricting coleoptile and seedling growth. Using large‐scale field trials with an extensive collection of barley accessions, we showed that a natural GA3ox1 haplotype moderately reduced plant height by 5–10 cm. We used CRISPR/Cas9 technology, generated several novel GA3ox1 mutants and validated the function of GA3ox1. We showed that altered GA3ox1 activities changed the level of active GA isoforms and consequently increased coleoptile length by an average of 8.2 mm, which could provide essential adaptation to maintain yield under climate change. We revealed that CRISPR/Cas9‐induced GA3ox1 mutations increased seed dormancy to an ideal level that could benefit the malting industry. We conclude that selecting HvGA3ox1 alleles offers a new opportunity for developing barley varieties with optimal stature, longer coleoptile and additional agronomic traits.

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An overview of floral regulatory genes in annual and perennial plants

Rehman

Bahadur

Xia

2023

Gene

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Genomic structural equation modelling provides a whole-system approach for the future crop breeding

Cited by 5 publications

References 54 publications

Pleiotropy Structures Plant Height and Seed Weight Scaling in Barley despite Long History of Domestication and Breeding Selection

Pleiotropy Structures Plant Height and Seed Weight Scaling in Barley despite Long History of Domestication and Breeding Selection

New semi‐dwarfing alleles with increased coleoptile length by gene editing of gibberellin 3‐oxidase 1 using CRISPR‐Cas9 in barley (Hordeum vulgare L.)

An overview of floral regulatory genes in annual and perennial plants

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