CUBIC: an atlas of genetic architecture promises directed maize improvement

Liu, Haijun; Wang, Xiaqing; Xiao, Yingjie; Luo, Jingyun; Qiao, Feng; Yang, Wenyu; Zhang, Ruyang; Meng, Yijiang; Sun, Jiamin; Yan, Shijuan; Peng, Yong; Niu, Luyao; Jian, Liumei; Song, Wei; Yan, Jiali; Li, Chunhui; Zhao, Yanxin; Ya, Liu; Warburton, Marilyn L.; Zhao, Jiuran

doi:10.1186/s13059-020-1930-x

Cited by 71 publications

(62 citation statements)

References 79 publications

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“…The trait mean values of culms for each accession (12 culms in 2014 and six culms in 2015 for each accession) were calculated. To reduce the effect of environment on phenotypic data, best linear unbiased prediction (BLUP) value for each trait was calculated based on the phenotypic data across two years using R package ‘lme4’ (Fang et al ., 2017; Liu et al ., 2020; Wang et al ., 2019).…”

Section: Methodsmentioning

confidence: 99%

“…We calculated the trait mean values of all the harvested culms for each accession in each year and then calculated the broad‐sense heritability ( H 2 ) as: H 2 = V G /( V G + V e / N ), where V G and V e represented genetic and residual variance, respectively; N was the number of years ( N = 2 in this study) (Liu et al ., 2020). The V G and Ve were estimated by treating genotype and environment as random effects in the mixed linear model.…”

Section: Methodsmentioning

confidence: 99%

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Genetic analyses of lodging resistance and yield provide insights into post‐Green‐Revolution breeding in rice

Guo

Xiao

Zhang

et al. 2020

Plant Biotechnology Journal

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Summary Lodging reduces grain yield in cereal crops. Understanding the genetic basis of lodging resistance (LR) benefits LR breeding. In the study, 524 accessions from a rice germplasm collection and 193 recombinant inbred lines were phenotyped for 17 LR‐related traits. Height and culm strength (the magnitude of applied force necessary to break the culm) were two major factors affecting LR. We conducted genome‐wide association study (GWAS) and identified 127 LR‐associated loci. Significant phenotypic correlations between culm‐strength traits and yield‐related traits were observed. To reveal the genetic relationship between them, we conducted GWAS of culm‐strength traits with adding yield‐related trait as a covariate and detected 63 loci linking culm strength and yield. As a proof, a near‐isogenic line for an association locus on chromosome 7 showed enhanced LR and yield. Strikingly, 58 additional loci were identified in the covariate‐added GWAS. Several LR‐associated loci had undergone divergent selection. Linkage analysis supported the GWAS results. We propose that introgression of alleles beneficial for both culm strength and panicle weight without negative effects on panicle number or pyramiding high‐yielding alleles and lodging‐resistant alleles without effects on yield can be employed for the post‐Green‐Revolution breeding.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Genetic analyses of lodging resistance and yield provide insights into post‐Green‐Revolution breeding in rice

Guo

Xiao

Zhang

et al. 2020

Plant Biotechnology Journal

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“…We constructed 30 F 1 populations by crossing 1428 previously reported inbred lines from the CUBIC (Complete-diallel plus Unbalanced Breeding-derived Inter-Cross) synthetic population as a maternal pool [ 34 ] with 30 paternal testers from diverse heterotic groups. We performed genome-wide association studies (GWAS) on all populations to identify heterosis and trait-associated genes involved in maize improvement.…”

Section: Introductionmentioning

confidence: 99%

The genetic mechanism of heterosis utilization in maize improvement

et al. 2021

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Background In maize hybrid breeding, complementary pools of parental lines with reshuffled genetic variants are established for superior hybrid performance. To comprehensively decipher the genetics of heterosis, we present a new design of multiple linked F1 populations with 42,840 F1 maize hybrids, generated by crossing a synthetic population of 1428 maternal lines with 30 elite testers from diverse genetic backgrounds and phenotyped for agronomic traits. Results We show that, although yield heterosis is correlated with the widespread, minor-effect epistatic QTLs, it may be resulted from a few major-effect additive and dominant QTLs in early developmental stages. Floral transition is probably one critical stage for heterosis formation, in which epistatic QTLs are activated by paternal contributions of alleles that counteract the recessive, deleterious maternal alleles. These deleterious alleles, while rare, epistatically repress other favorable QTLs. We demonstrate this with one example, showing that Brachytic2 represses the Ubiquitin3 locus in the maternal lines; in hybrids, the paternal allele alleviates this repression, which in turn recovers the height of the plant and enhances the weight of the ear. Finally, we propose a molecular design breeding by manipulating key genes underlying the transition from vegetative-to-reproductive growth. Conclusion The new population design is used to dissect the genetic basis of heterosis which accelerates maize molecular design breeding by diminishing deleterious epistatic interactions.

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“…However, most of the lead SNPs were heterozygous and multiple haplotypes had been detected in the candidate regions, rendering it highly difficult to effectively identify favorable functional alleles. Moreover, previous research has shown that allelic heterogeneity may lead to misleading association and missing heritability (Yano et al ., 2016; Liu et al ., 2020). The haplotype information we provide here will thus be a valuable resource for future GWAS in tea plants.…”

Section: Discussionmentioning

confidence: 99%

A phased genome based on single sperm sequencing reveals crossover pattern and complex relatedness in tea plants

et al. 2020

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SUMMARYFor diploid organisms that are highly heterozygous, a phased haploid genome can greatly aid in functional genomic, population genetic and breeding studies. Based on the genome sequencing of 135 single sperm cells of the elite tea cultivar ‘Fudingdabai’, we herein phased the genome of Camellia sinensis, one of the most popular beverage crops worldwide. High‐resolution genetic and recombination maps of Fudingdabai were constructed, which revealed that crossover (CO) positions were frequently located in the 5′ and 3′ ends of annotated genes, while CO distributions across the genome were random. The low CO frequency in tea can be explained by strong CO interference, and CO simulation revealed the proportion of interference insensitive CO ranged from 5.2% to 11.7%. We furthermore developed a method to infer the relatedness between tea accessions and detected complex kinship and genetic signatures of 106 tea accessions. Among them, 59 accessions were closely related with Fudingdabai and 31 of them were first‐degree relatives. We additionally identified genes displaying allele specific expression patterns between the two haplotypes of Fudingdabai and genes displaying significantly differential expression levels between Fudingdabai and other haplotypes. These results lay the foundation for further investigation of genetic and epigenetic factors underpinning the regulation of gene expression and provide insights into the evolution of tea plants as well as a valuable genetic resource for future breeding efforts.

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CUBIC: an atlas of genetic architecture promises directed maize improvement

Cited by 71 publications

References 79 publications

Genetic analyses of lodging resistance and yield provide insights into post‐Green‐Revolution breeding in rice

Genetic analyses of lodging resistance and yield provide insights into post‐Green‐Revolution breeding in rice

The genetic mechanism of heterosis utilization in maize improvement

A phased genome based on single sperm sequencing reveals crossover pattern and complex relatedness in tea plants

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