Genomic selection and genetic architecture of agronomic traits during modern rapeseed breeding

Hu, Jihong; Zhao, Jing; Zhang, Fugui; Xie, Ting; Xu, Kun; Gao, Guizhen; Yan, Guiqin; Li, Hongge; Li, Lixia; Ji, Gaoxiang; An, Hong; Li, Hao; Huang, Qian; Zhang, Meili; Wu, Jinfeng; Song, Weilin; Zhang, Xiaojun; Luo, Yuqin; Pires, J. Chris; Batley, Jacqueline; Tian, Shilin; Wu, Xiaoming

doi:10.1038/s41588-022-01055-6

Cited by 83 publications

(70 citation statements)

References 74 publications

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“…Dark jute originated in Africa and was domesticated in Asia (Kundu et al., 2013), which have obvious geographical differences. It is widely reported that crop breeding has undergone two important stages: domestication and improvement (Hu et al., 2022; Zhou et al., 2015). To identify the potential selective genes of the two breeding stages in jute, we applied a cross‐population composite likelihood ratio (XP‐CLR; Chen et al., 2010) and F ST to test for two comparative patterns (i.e.…”

Section: Resultsmentioning

confidence: 99%

Multi‐omics provides new insights into the domestication and improvement of dark jute (Corchorus olitorius)

Yang

Tian

et al. 2022

The Plant Journal

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SUMMARY Jute (Corchorus sp.) is the most important bast fiber crop worldwide; however, the mechanisms underlying domestication and improvement remain largely unknown. We performed multi‐omics analysis by integrating de novo sequencing, resequencing, and transcriptomic and epigenetic sequencing to clarify the domestication and improvement of dark jute Corchorus olitorius. We demonstrated that dark jute underwent early domestication and a relatively moderate genetic bottleneck during improvement breeding. A genome‐wide association study of 11 important agronomic traits identified abundant candidate loci. We characterized the selective sweeps in the two breeding stages of jute, prominently, soil salinity differences played an important role in environmental adaptation during domestication, and the strongly selected genes for improvement had an increased frequency of favorable haplotypes. Furthermore, we speculated that an encoding auxin/indole‐3‐acetic acid protein COS07g_00652 could enhance the flexibility and strength of the stem to improve fiber yield. Our study not only provides valuable genetic resources for future fiber breeding in jute, but also is of great significance for reviewing the genetic basis of early crop breeding.

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Section: Resultsmentioning

confidence: 99%

Multi‐omics provides new insights into the domestication and improvement of dark jute (Corchorus olitorius)

Yang

Tian

et al. 2022

The Plant Journal

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“…Likewise, the expression of BnaJAZs belonging to group IV (homologous to AtJAZ11 / 12 ) was up-regulated, but the degree of which in susceptible was higher than that in resistant ( Figure 5 B). Because the expression differential fold of BnaJAZs belonging to group IV between inoculation and un-inoculation was very small, we further performed the SNPs and SVs detection only in BnaJAZs of group I and BnaA02T0200100ZS using the whole genome re-sequencing data including 418 rapeseed accessions [ 30 ]. A total of 17 SNPs were detected in four BnaJAZs, and three SVs were detected in two BnaJAZs .…”

Section: Resultsmentioning

confidence: 99%

Genome-Wide Identification and Variation Analysis of JAZ Family Reveals BnaJAZ8.C03 Involved in the Resistance to Plasmodiophora brassicae in Brassica napus

Guan

et al. 2022

IJMS

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Clubroot caused by Plasmodiophora brassicae led to a significant decrease in the yield and quality of Brassica napus, one of the most important oil crops in the world. JAZ proteins are an essential repressor of jasmonates (JAs) signaling cascades, which have been reported to regulate the resistance to P. brassicae in B. napus. In this study, we identified 51, 25 and 26 JAZ proteins in B. napus, B. rapa and B. oleracea, respectively. Phylogenetic analysis displayed that the notedJAZ proteins were divided into six groups. The JAZ proteins clustered in the same group shared a similar motif composition and distribution order. The 51 BnaJAZs were not evenly assigned on seventeen chromosomes in B. napus, except for A04 and C07. The BnaJAZs of the AtJAZ7/AtJAZ8 group presented themselves to be significantly up-regulated after inoculation by P. brassicae. Variation analysis in a population with a specific resistance performance in P. brassicae displayed a 64 bp translocation in BnaC03T0663300ZS (BnaJAZ8.C03, homologous to AtJAZ8) with an 8% reduction in the disease index on average. Through protein–protein interaction analysis, 65 genes were identified that might be involved in JAZ8 regulation of resistance to P. brassicae in B. napus, which provided new clues for understanding the resistance mechanism to P. brassicae.

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“…Although numerous studies have focused on seed yield genetic improvement of rapeseed through quantitative trait locus (QTL) mapping, high-throughput sequencing, and genotyping techniques ( Yang et al, 2012 ; Liu et al, 2015b ; Zhao et al, 2016 ; Shah et al, 2018 ; Zheng et al, 2020 ; Khan et al, 2021 ; Hu et al, 2022 ), the comprehensive study of seed development and the mechanism contributing to high yield in the high-yield field, especially the Xiangride area, Tsaldam Basin of Qinghai Province in China, is poor, which is a constraint to our in-depth understanding of the environmental influences of this important trait and provides valuable information for future rapeseed breeding.…”

Section: Discussionmentioning

confidence: 99%

“…Both direct yield component traits and indirect yield-related traits are elaborately controlled by several genes and are highly influenced by environmental conditions ( Van Camp, 2005 ; Shi et al, 2009 ; Ding et al, 2012 ; Zhao et al, 2016 ; Lu et al, 2017 ). The identification of yield candidate genes implies the detection of important genes for agricultural and economic quantitative traits ( Raboanatahiry et al, 2018 , 2022 ; Hu et al, 2021 , 2022 ; Pal et al, 2021 ; Zheng et al, 2022 ). In the model plant Arabidopsis thaliana , 425 genes were collected from the TAIR website 2 to be related to flowering time, plant height, branch number, seed number, seed weight, and SY ( Shi et al, 2009 ).…”

Section: Discussionmentioning

confidence: 99%

“…Based on the construction of a quantitative genomic map of Brassica napus , Raboanatahiry further revealed 517 regions of overlapping QTLs that harbored 2,744 candidate genes and might affect multiple traits simultaneously ( Raboanatahiry et al, 2022 ). Hu unraveled the genomic basis for the selection of adaptation and agronomic traits and identified 628 associated locus-related causative candidate genes for 56 agronomically important traits (including plant architecture and yield traits) through genome-wide association studies ( Hu et al, 2022 ). In this study, we used these rapeseed candidate yield-related genes in our transcriptome data analysis and the results showed that the DEGs related to yield traits were generally scattered changes, which means that the high-yield environment may affect rapeseed yield indirectly.…”

Section: Discussionmentioning

confidence: 99%

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Transcriptomic analysis of rapeseed (Brassica napus. L.) seed development in Xiangride, Qinghai Plateau, reveals how its special eco-environment results in high yield in high-altitude areas

et al. 2022

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As one of the most important oil crops, rapeseed (Brassica napus) is cultivated worldwide to produce vegetable oil, animal feed, and biodiesel. As the population grows and the need for renewable energy increases, the breeding and cultivation of high-yield rapeseed varieties have become top priorities. The formation of a high rapeseed yield is so complex because it is influenced not only by genetic mechanisms but also by many environmental conditions, such as climatic conditions and different farming practices. Interestingly, many high-yield areas are located in special eco-environments, for example, in the high-altitude Xiangride area of the Qinghai Plateau. However, the molecular mechanisms underlying the formation of high yields in such a special eco-environment area remain largely unknown. Here, we conducted field yield analysis and transcriptome analysis in the Xiangride area. Compared with the yield and environmental factors in the Xinning area (a low-yielding area), we found that the relatively longer daylight length is the key to high rapeseed yield in the Xiangride area, which leads up to a 52.1% increase in rapeseed yield, especially the increase in thousand seed weight and silique number (SN). Combined with transcriptome H-cluster analysis and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional analyses, we can assume that the grain development of rapeseed in the Xiangride area is ahead of schedule and lasts for a long time, leading to the high-yield results in the Xiangride area, confirmed by the expression analysis by quantitative real-time polymerase chain reaction (qRT-PCR) of yield-related genes. Our results provide valuable information for further exploring the molecular mechanism underlying high yield in special ecological environments and provide a helpful reference for studying seed development characteristics in special-producing regions for Brassica napus.

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Genomic selection and genetic architecture of agronomic traits during modern rapeseed breeding

Cited by 83 publications

References 74 publications

Multi‐omics provides new insights into the domestication and improvement of dark jute (Corchorus olitorius)

Multi‐omics provides new insights into the domestication and improvement of dark jute (Corchorus olitorius)

Genome-Wide Identification and Variation Analysis of JAZ Family Reveals BnaJAZ8.C03 Involved in the Resistance to Plasmodiophora brassicae in Brassica napus

Transcriptomic analysis of rapeseed (Brassica napus. L.) seed development in Xiangride, Qinghai Plateau, reveals how its special eco-environment results in high yield in high-altitude areas

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