Please wait a minute...
Journal of Integrative Agriculture
Advanced Online Publication | Current Issue | Archive | Adv Search
Genome-wide association study integrated with transcriptome analysis to identify boron efficiency-related candidate genes and favorable haplotypes in Brassica napus L.

Ziwei Zhang1, 2, Haoqiang Zhai3, Yingpeng Hua4, Sheliang Wang2, Fangsen Xu1, 2#

1 National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
2 Microelement Research Center, College of Resources & Environment, Huazhong Agricultural University, Wuhan 430070, China

3 Hubei Yishizhuang Agricultural Technology Company, Yichang 443000, China

4 School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China

Download:  PDF in ScienceDirect  
Export:  BibTeX | EndNote (RIS)      
摘要  

油菜(Brassica napus L.)是全球重要的油料作物之一,我国大力推广种植甘蓝型油菜B是植物生长发育必需微量营养元素,我国甘蓝型油菜种植区土壤普遍缺硼或严重缺硼。因此,提高油菜的抗缺硼能力成为一个重要的育种目标。然而,目前关于硼高效相关性状变异的遗传基础尚不清楚,能用于遗传育种的优异等位基因变异有待系统深入研究。本研究以391甘蓝型油菜自然群体品种为材料,通过营养液培养的方法考察硼高效相关性状,包括相对根长(RRL)、地上部干重(SDW)、根部干重(RDW)和硼效率系数(BEC),这些性状在缺硼条件下表现出广泛的表型变异。结合全基因组重测序获得的高密度SNP标记进行全基因组关联分析(GWAS),使用一般线性模型和混合线性模型,共鉴定106显著关联的SNP位点其中,在低硼条件下多个性状的三次重复试验中,检测到chrA03:14087835–14764672chrC03:20110319–22135492两个显著的SNP簇。结合转录组分析,四个基因BnaA03g29020DBnaA03g29440DBnaC03g33010D  BnaC03g34490D)在启动子区域或编码区内具有优异单倍型,并表现出更高的差异表达倍数,被鉴定为可能参与硼高效利用的候选基因。这些优异单倍型在硼缺乏条件下促进了苗期生长与油菜产量。鉴于我国硼矿资源缺乏,快速准确地鉴定到更多的硼高效优异等位基因并用于作物响应硼胁迫遗传机制研究,对于培育硼高效利用的甘蓝型油菜品种以促进油菜绿色可持续的农业生产具有重要的理论和实践意义。



Abstract  

Rapeseed (Brassica napus L.) is a major oil crop worldwide that is vigorously promoted for cultivation in China.  Boron (B) is an essential micronutrient for plant growth and development.  However, agricultural soils in rapeseed planting areas often show either B deficiency or severe B deficiency.  Increasing the resistance to B deficiency is a pivotal goal in the breeding of rapeseed, yet the genetic basis for variations in B efficiency-related traits remains unclear. In this study, a natural population with 391 rapeseed accessions was used to investigate B efficiency-related traits through a nutrient solution system, including relative root length (RRL), shoot dry weight (SDW), root dry weight (RDW), and B efficiency coefficient (BEC), which exhibited extensive phenotypic variations under B deficiency.  Through a genome-wide association study (GWAS) of B efficiency-related traits using high-density SNP markers obtained from whole-genome resequencing, we identified 106 significantly associated SNPs by employing both the general linear model and the mixed linear model.  Among these SNP loci, two prominent SNP clusters were detected on chrA03:14087835–14764672 and chrC03:20110319–22135492 at low B level across three repeated experiments of multiple traits.  Integrated with the transcriptome analysis, four genes, BnaA03g29020D, BnaA03g29440D, BnaC03g33010D, and BnaC03g34490D, exhibiting higher differentially expressed fold-change along with favorable haplotypes within the promoter or coding region were identified as candidate genes that could potentially be involved in B efficient utilization, and their favorable haplotypes improved seedling growth and productivity under B deficiency.  In view of the lack of B mineral resources in China, rapid and accurate identification of more B-efficient alleles and the study of the genetic mechanism underlying crops in response to B deficiency have important theoretical and practical significance for cultivating B-efficient varieties and maintaining green, sustainable agriculture quickly and accurately.

Keywords:  rapeseed       boron deficiency              GWAS              transcriptomic analysis              favorable haplotypes              B efficiency  
Online: 12 November 2024  
Fund: 

This work was supported by the National Natural Science Foundation of China (32372805 and 31972483). 

About author:  #Correspondences Fangsen Xu, E-mail: fangsenxu@mail.hzau.edu.cn

Cite this article: 

Ziwei Zhang, Haoqiang Zhai, Yingpeng Hua, Sheliang Wang, Fangsen Xu. 2024. Genome-wide association study integrated with transcriptome analysis to identify boron efficiency-related candidate genes and favorable haplotypes in Brassica napus L.. Journal of Integrative Agriculture, Doi:10.1016/j.jia.2024.11.013

Alexander D H, Novembre J, Lange K. 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome Research, 19, 1655–1664.

Begum R A, Fry S C. 2022. Boron bridging of rhamnogalacturonan-II in Rosa and Arabidopsis cell cultures occurs mainly in the endo-membrane system and continues at a reduced rate after secretion. Annals of Botany, 130, 703–715.

Bell E M, Lin W C, Husbands A Y, Yu L, Jaganatha V, Jablonska B, Mangeon A, Neff M M, Girke T, Springer P S. 2012. Arabidopsis LATERAL ORGAN BOUNDARIES negatively regulates brassinosteroid accumulation to limit growth in organ boundaries. Proceedings of the National Academy of Sciences of the United States of America, 109, 21146–21151.

Bradbury P J, Zhang Z, Kroon D E, Casstevens T M, Ramdoss Y, Buckler E S. 2007. TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics, 23, 2633–2635.

Brown P H, Bellaloui N, Wimmer M A, Bassil E S, Ruiz J, Hu H, Pfeffer H, Dannel F, Römheld V. 2002. Boron in plant biology. Plant Biology, 4, 205–223.

Brown P H, Shelp B J. 1997. Boron mobility in plants. Plant and Soil, 193, 85–101.

Bureau M, Rast M I, Illmer J, Simon R. 2010. JAGGED LATERAL ORGAN (JLO) controls auxin dependent patterning during development of the Arabidopsis embryo and root. Plant Molecular Biology, 74, 479–491.

Cai D, Xiao Y, Yang W, Ye W, Wang B, Younas M, Wu J, Liu K. 2014. Association mapping of six yield-related traits in rapeseed (Brassica napus L.). Theoretical and Applied Genetics, 127, 85–96.

Camacho-Cristóbal J J, Rexach J, González-Fontes A. 2008. Boron in plants: Deficiency and toxicity. Journal of Integrative Plant Biology, 50, 1247–1255.

Chen R, Deng Y, Ding Y, Guo J, Qiu J, Wang B, Wang C, Xie Y, Zhang Z, Chen J, Chen L, Chu C, He G, He Z, Huang X, Xing Y, Yang S, Xie D, Liu Y, Li J. 2022. Rice functional genomics: Decades’ efforts and roads ahead. Science China Life Sciences, 65, 33–92.

Cheng F, Liu S, Wu J, Fang L, Sun S, Liu B, Li P, Hua W, Wang X. 2011. BRAD, the genetics and genomics database for Brassica plants. BMC Plant Biology, 11, 136.

Chormova D, Messenger D J, Fry S C. 2014. Rhamnogalacturonan-II cross-linking of plant pectins via boron bridges occurs during polysaccharide synthesis and/or secretion. Plant Signaling & Behavior, 9, e28169.

Dinka S J, Campbell M A, Demers T, Raizada M N. 2007. Predicting the size of the progeny mapping population required to positionally clone a gene. Genetics, 176, 2035–2054.

Fu W, Zhao L, Qiu W, Xu X, Ding M, Lan L, Qu S, Wang S. 2024. Whole-genome resequencing identifies candidate genes and allelic variation in the MdNADP-ME promoter that regulate fruit malate and fructose contents in apple. Plant Communicaiton, 14, 100973.

He M, Wang S, Zhang C, Liu L, Zhang J, Qiu S, Wang H, Yang G, Xue S, Shi L, Xu F. 2021. Genetic variation of BnaA3.NIP5;1 expressing in the lateral root cap contributes to boron deficiency tolerance in Brassica napusPlos Genetics, 17, e1009661.

He M, Zhang C, Chu L, Wang S, Shi L, Xu F. 2021. Specific and multiple-target gene silencing reveals function diversity of BnaA2.NIP5;1 and BnaA3.NIP5;1 in Brassica napus. Plant, Cell & Environment, 44, 3184–3194.

Hu J, Chen B, Zhao J, Zhang F, Xie T, Xu K, Gao G, Yan G, Li H, Li L, Ji G, An H, Li H, Huang Q, Zhang M, Wu J, Song W, Zhang X, Luo Y, Chris Pires J, et al. 2022. Genomic selection and genetic architecture of agronomic traits during modern rapeseed breeding. Nature Genetics, 54, 694–704.

Hua Y, Feng Y, Zhou T, Xu F. 2017. Genome-scale mRNA transcriptomic insights into the responses of oilseed rape (Brassica napus L.) to varying boron availabilities. Plant and Soil, 416, 205–225.

Hua Y, Zhang D, Zhou T, He M, Ding G, Shi L, Xu F. 2016a. Transcriptomics-assisted quantitative trait locus fine mapping for the rapid identification of a nodulin 26-like intrinsic protein gene regulating boron efficiency in allotetraploid rapeseed. Plant, Cell & Environment, 39, 1601–1618.

Hua Y, Zhou T, Ding G, Yang Q, Shi L, Xu F. 2016b. Physiological, genomic and transcriptional diversity in responses to boron deficiency in rapeseed genotypes. Journal of Experimental Botany, 67, 5769–5784.

Huang L, Min Y, Schiessl S, Xiong X, Jan H U, He X, Qian W, Guan C, Snowdon R J, Hua W, Guan M, Qian L. 2021. Integrative analysis of GWAS and transcriptome to reveal novel loci regulation flowering time in semi-winter rapeseed. Plant Science, 310, 110980.

Kong W, An B, Zhang Y, Yang J, Li S, Sun T, Li Y. 2019. Sugar transporter proteins (STPs) in gramineae crops: Comparative analysis, phylogeny, evolution, and expression profiling. Cells, 8, 560.

Körber N, Bus A, Li J, Parkin I A P, Wittkop B, Snowdon R J, Stich B. 2016. Agronomic and seed quality traits dissected by genome-wide association mapping in Brassica napus. Frontiers in Plant Science, 7, 386.

Lin M, Islamov B, Aleliūnas A, Armonienė R, Gorash A, Meigas E, Ingver A, Tamm I, Kollist H, Strazdiņa V, Bleidere M, Brazauskas G, Lillemo M. 2024. Genome-wide association analysis identifies a consistent QTL for powdery mildew resistance on chromosome 3A in Nordic and Baltic spring wheat. Theoretical and Applied Genetics, 137, 25.

Liu T, Bao C, Ban Q, Wang C, Hu T, Wang J. 2022. Genome-wide identification of sugar transporter gene family in Brassicaceae crops and an expression analysis in the radish. BMC Plant Biology, 22, 245.

Livak K J, Schmittgen T D. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods, 25, 402–408.

Lu K, Peng L, Zhang C, Lu J, Yang B, Xiao Z, Liang Y, Xu X, Qu C, Zhang K, Liu L, Zhu Q, Fu M, Yuan X, Li J. 2017. Genome-wide association and transcriptome analyses reveal candidate genes underlying yield-determining traits in Brassica napus. Frontiers in Plant Science, 8, 206.

Lu K, Wei L, Li X, Wang Y, Wu J, Liu M, Zhang C, Chen Z, Xiao Z, Jian H, Cheng F, Zhang K, Du H, Cheng X, Qu C, Qian W, Liu L, Wang R, Zou Q, Ying J, et al. 2019. Whole-genome resequencing reveals Brassica napus origin and genetic loci involved in its improvement. Nature Communication, 10, 1154.

Lu K, Xiao Z, Jian H, Peng L, Qu C, Fu M, He B, Tie L, Liang Y, Xu X, Li J. 2016. A combination of genome-wide association and transcriptome analysis reveals candidate genes controlling harvest index-related traits in Brassica napus. Scientific Reports, 6, 36452.

Naito T, Yamashino T, Kiba T, Koizumi N, Kojima M, Sakakibara H, Mizuno T. 2007. A link between cytokinin and ASL9 (ASYMMETRIC LEAVES 2 LIKE 9) that belongs to the AS2/LOB (LATERAL ORGAN BOUNDARIES) family genes in Arabidopsis thaliana. Bioscience, Biotechnology, and Biochemistry, 71, 1269–1278.

Onuh A F, Miwa K. 2021. Regulation, diversity and evolution of boron transporters in plants. Plant and Cell Physiology, 62, 590–599.

Pal L, Sandhu S K, Bhatia D, Sethi S. 2021. Genome-wide association study for candidate genes controlling seed yield and its components in rapeseed (Brassica napus L.). Physiology and Molecular Biology of Plants, 27, 1933–1951.

Piepho H P, Büchse A, Emrich K. 2003. A Hitchhiker’s guide to mixed models for randomized experiments. Journal of Agronomy and Crop Science, 189, 310–322.

Prince S J, Valliyodan B, Ye H, Yang M, Tai S, Hu W, Murphy M, Durnell L A, Song L, Joshi T, Liu Y, Van de Velde J, Vandepoele K, Grover Shannon J, Nguyen H T. 2019. Understanding genetic control of root system architecture in soybean: Insights into the genetic basis of lateral root number. Plant, Cell & Environment, 42, 212–229.

Qian M, Fan Y, Li Y, Liu M, Sun W, Duan H, Yu M, Chang W, Niu Y, Li X, Liang Y, Qu C, Li J, Lu K. 2021. Genome-wide association study and transcriptome comparison reveal novel QTL and candidate genes that control petal size in rapeseed. Journal of Experimental Botany, 72, 3597–3610.

Schoenaers S, Lee H K, Gonneau M, Faucher E, Levasseur T, Akary E, Claeijs N, Moussu S, Broyart C, Balcerowicz D, AbdElgawad H, Bassi A, Damineli D S C, Costa A, Feijó J A, Moreau C, Bonnin E, Cathala B, Santiago J, Höfte H, et al. 2024. Rapid alkalinization factor 22 has a structural and signaling role in root hair cell wall assembly. Nature Plants, 10, 494–511.

Scholz-Starke J, Büttner M, Sauer N. 2003. AtSTP6, a new pollen-specific H+-monosaccharide symporter from Arabidopsis. Plant Physiology, 131, 70–77.

Shen X, Song S, Li C, Zhang J. 2022. Synonymous mutations in representative yeast genes are mostly strongly non-neutral. Nature, 606, 725–731.

Takano J, Miwa K, Yuan L, von Wirén N, Fujiwara T. 2005. Endocytosis and degradation of BOR1, a boron transporter of Arabidopsis thaliana, regulated by boron availability. Proceedings of the National Academy of Sciences of the United States of America, 102, 12276–12281.

Takano J, Noguchi K, Yasumori M, Kobayashi M, Gajdos Z, Miwa K, Hayashi H, Yoneyama T, Fujiwara T. 2002. Arabidopsis boron transporter for xylem loading. Nature, 420, 337–340.

Takano J, Tanaka M, Toyoda A, Miwa K, Kasai K, Fuji K, Onouchi H, Naito S, Fujiwara T. 2010. Polar localization and degradation of Arabidopsis boron transporters through distinct trafficking pathways. Proceedings of the National Academy of Sciences of the United States of America, 107, 5220–5225.

Takano J, Wada M, Ludewig U, Schaaf G, von Wirén N, Fujiwara T. 2006. The Arabidopsis major intrinsic protein NIP5;1 is essential for efficient boron uptake and plant development under boron limitation. The Plant Cell, 18, 1498–1509.

Tan H, Xiang X, Tang J, Wang X. 2016. Nutritional functions of the funiculus in Brassica napus seed maturation revealed by transcriptome and dynamic metabolite profile analyses. Physiology and Molecular Biology of Plants, 92, 539–553.

Tanaka M, Fujiwara T. 2008. Physiological roles and transport mechanisms of boron: Perspectives from plants. Pflügers Archiv (European Journal of Physiology), 456, 671–677.

Tanaka M, Wallace I S, Takano J, Roberts D M, Fujiwara T. 2008. NIP6;1 is a boric acid channel for preferential transport of boron to growing shoot tissues in Arabidopsis. The Plant Cell, 20, 2860–2875.

Tang S, Zhao H, Lu S, Yu L, Zhang G, Zhang Y, Yang QY, Zhou Y, Wang X, Ma W, Xie W, Guo L. 2021. Genome- and transcriptome-wide association studies provide insights into the genetic basis of natural variation of seed oil content in Brassica napus. Molecular Plant, 14, 470–487.

Thatcher L F, Powell J J, Aitken E A B, Kazan K, Manners J M. 2012. The lateral organ boundaries domain transcription factor LBD20 functions in fusarium wilt susceptibility and jasmonate signaling in Arabidopsis. Plant Physiology, 160, 407–418.

U.S. Department of Agriculture (USDA), Economic Research Service (ERS). Oil crops yearbook. [2024-3-25]. https://www.ers.usda.gov/data-products/oil-crops-yearbook/

Wang Y, Shi L, Cao X, Xu F. 2007. Boron nutrition and boron application in crops. In: Xu F, Goldbach H E, Brown P H, Bell R W, Fujiwara T, Hunt C D, Goldberg S, Shi L, eds., Advances in Plant and Animal Boron Nutrition: Proceedings of the 3rd International Symposium on all Aspects of Plant and Animal Boron Nutrition. Springer Publishing, Dordrecht, Netherlands. pp. 93101.

Warington K. 1923. The effect of boric acid and borax on the broad bean and certain other plants. Annals of Botany, os-37, 629–672.

Wu D, Liang Z, Yan T, Xu Y, Xuan L, Tang J, Zhou G, Lohwasser U, Hua S, Wang H, Chen X, Wang Q, Zhu L, Maodzeka A, Hussain N, Li Z, Li X, Shamsi I H, Jilani G, Wu L, et al. 2019. Whole-genome resequencing of a worldwide collection of rapeseed accessions reveals the genetic basis of ecotype divergence. Molecular Plant, 12, 30–43.

Xiao Y, Liu H, Wu L, Warburton M, Yan J. 2017. Genome-wide association studies in maize: Praise and stargaze. Molecular Plant, 10, 359–374.

Xu F, Wang Y, Ying W, Meng J. 2002. Inheritance of boron nutrition efficiency in Brassica napus. Journal of Plant Nutrition, 25, 901–912.

Xu F, Wang Y, Meng J. 2001. Mapping boron efficiency gene(s) in Brassica napus using RFLP and AFLP markers. Plant Breeding, 120, 319–324.

Yuan P, Liu H, Wang X, Hammond J P, Shi L. 2023. Genome-wide association study reveals candidate genes controlling root system architecture under low phosphorus supply at seedling stage in Brassica napus. Molecular Breeding, 43, 63.

Zhang C, Dong S, Xu J, He W, Yang T. 2019. PopLDdecay: A fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Bioinformatics, 35, 1786–1788.

Zhang C, He M, Jiang Z, Liu L, Pu J, Zhang W, Wang S, Xu F. 2022. The xyloglucan endotransglucosylase/hydrolase gene XTH22/TCH4 regulates plant growth by disrupting the cell wall homeostasis in Arabidopsis under boron deficiency. International Journal of Molecular Sciences, 23, 1250.

Zhang D, Hua Y, Wang X, Zhao H, Shi L, Xu F. 2014a. A high-density genetic map identifies a novel major qtl for boron efficiency in oilseed rape (Brassica napus L.). PLoS ONE, 9, e112089.

Zhang D, Zhao H, Shi L, Xu F. 2014b. Physiological and genetic responses to boron deficiency in Brassica napus: A review. Soil Science and Plant Nutrition, 60, 304–313. 

Zhao H, Shi L, Duan X, Xu F, Wang Y, Meng J. 2008. Mapping and validation of chromosome regions conferring a new boron-efficient locus in Brassica napus. Molecular Breeding, 22, 495–506.

Zhao Z, Wu L, Nian F, Ding G, Shi T, Zhang D, Shi L, Xu F, Meng J. 2012. Dissecting quantitative trait loci for boron efficiency across multiple environments in Brassica napus. PLoS ONE, 7, e45215.

Zhou T, Hua Y, Huang Y, Ding G, Shi L, Xu F. 2016. Physiological and transcriptional analyses reveal differential phytohormone responses to boron deficiency in brassica napus genotypes. Frontiers in Plant Science, 7, 221.

No related articles found!
No Suggested Reading articles found!