Genome-wide Identification, Classification, Expression and Duplication Analysis of GRAS Family Genes in Juglans regia L.

Abstract Background: Walnut anthracnose caused by Colletotrichum gloeosporioides (Penz.) Penz. and Sacc. is an important walnut production problem in China. Although the long non-coding RNAs (lncRNAs) are important for plant disease resistance , the molecular mechanisms underlying resistance to C. gloeosporioides in walnut remain poorly understood.Results: The anthracnose-resistant F26 fruits from the B26 clone and the anthracnose-susceptible F423 fruits from the 4-23 clone of walnut were used as the test materials. Specifically, we performed a comparative transcriptome analysis of F26 and F423 fruit bracts to identify differentially expressed LncRNAs (DELs) at five time-points (tissues at 0 hpi, pathological tissues at 24 hpi, 48 hpi, 72 hpi, and distal uninoculated tissues at 120 hpi). Compared with F423, a total of 14525 DELs were identified, including 10645 upregulated lncRNAs and 3846 downregulated lncRNAs in F26. The number of upregulated lncRNAs in F26 compared to in F423 was significantly higher at the early stages of C. gloeosporioides infection. A total of 5 modules related to disease resistance were screened by WGCNA and the target genes of lncRNAs were obtained. Bioinformatic analysis showed that the target genes of upregulated lncRNAs were enriched in immune-related processes during the infection of C. gloeosporioides, such as activation of innate immune response, defense response to bacterium, incompatible interaction and immune system process, and enriched in plant hormone signal transduction, phenylpropanoid biosynthesis and other pathways. And 124 known target genes for 96 hub lncRNAs were predicted, including 10 known resistance genes. The expression of 5 lncRNAs and 5 target genes was confirmed by qPCR, which was consistent with the RNA-seq data.Conclusions: The results of this study provide the basis for future functional characterizations of lncRNAs regarding the C. gloeosporioides resistance of walnut fruit bracts.

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Major QTL with pleiotropic effects controlling time of leaf budburst and flowering-related traits in walnut (Juglans regia L.)

Scientific Reports ◽

10.1038/s41598-020-71809-x ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Şakir Burak Bükücü ◽

Mehmet Sütyemez ◽

Sina Kefayati ◽

Aibibula Paizila ◽

Abdulqader Jighly ◽

...

Keyword(s):

Genome Wide Association Study ◽

Juglans Regia ◽

Genotypic Variation ◽

Phenotypic Traits ◽

Juvenile Period ◽

Phenotypic Data ◽

Breeding Programs ◽

Genome Wide ◽

A Genome ◽

Major Qtl

Abstract Breeding studies in walnut (Juglans regia L.) are usually time consuming due to the long juvenile period and therefore, this study aimed to determine markers associated with time of leaf budburst and flowering-related traits by performing a genome-wide association study (GWAS). We investigated genotypic variation and its association with time of leaf budburst and flowering-related traits in 188 walnut accessions. Phenotypic data was obtained from 13 different traits during 3 consecutive years. We used DArT-seq for genotyping with a total of 33,519 (14,761 SNP and 18,758 DArT) markers for genome-wide associations to identify marker underlying these traits. Significant correlations were determined among the 13 different traits. Linkage disequilibrium decayed very quickly in walnut in comparison with other plants. Sixteen quantitative trait loci (QTL) with major effects (R2 between 0.08 and 0.23) were found to be associated with a minimum of two phenotypic traits each. Of these QTL, QTL05 had the maximum number of associated traits (seven). Our study is GWAS for time of leaf budburst and flowering-related traits in Juglans regia L. and has a strong potential to efficiently implement the identified QTL in walnut breeding programs.

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Genome wide identification and expression pattern analysis of the GRAS family in quinoa

Functional Plant Biology ◽

10.1071/fp21017 ◽

2021 ◽

Author(s):

Xiaolin Zhu ◽

Baoqiang Wang ◽

Xiaohong Wei

Keyword(s):

Expression Pattern ◽

Pattern Analysis ◽

Gras Family ◽

Expression Pattern Analysis ◽

Genome Wide

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Genome-Wide Association Study Reveals Candidate Genes Involved in Fruit Trait Variation in Persian Walnut (Juglans regia L.)

Frontiers in Plant Science ◽

10.3389/fpls.2020.607213 ◽

2021 ◽

Vol 11 ◽

Author(s):

Anthony Bernard ◽

Julie Crabier ◽

Armel S. L. Donkpegan ◽

Annarita Marrano ◽

Fabrice Lheureux ◽

...

Keyword(s):

Association Study ◽

Candidate Genes ◽

Fruit Quality ◽

Genome Wide Association Study ◽

Juglans Regia ◽

Snp Array ◽

Germplasm Collection ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome

Elucidating the genetic determinants of fruit quality traits in walnut is essential to breed new cultivars meeting the producers and consumers’ needs. We conducted a genome-wide association study (GWAS) using multi-locus models in a panel of 170 accessions of Juglans regia from the INRAE walnut germplasm collection, previously genotyped using the AxiomTMJ. regia 700K SNP array. We phenotyped the panel for 25 fruit traits related to morphometrics, shape, volume, weight, ease of cracking, and nutritional composition. We found more than 60 marker-trait associations (MTAs), including a highly significant SNP associated with nut face diameter, nut volume and kernel volume on chromosome 14, and 5 additional associations were detected for walnut weight. We proposed several candidate genes involved in nut characteristics, such as a gene coding for a beta-galactosidase linked to several size-related traits and known to be involved in fruit development in other species. We also confirmed associations on chromosomes 5 and 11 with nut suture strength, recently reported by the University of California, Davis. Our results enhance knowledge of the genetic control of important agronomic traits related to fruit quality in walnut, and pave the way for the development of molecular markers for future assisted selection.

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Genome-wide identification and characterization of long non-coding RNAs conferring resistance to Colletotrichum gloeosporioides in walnut (Juglans regia)

10.21203/rs.3.rs-36919/v4 ◽

2020 ◽

Author(s):

Shan Feng ◽

Hongcheng Fang ◽

Xia Liu ◽

Yuhui Dong ◽

Qingpeng Wang ◽

...

Keyword(s):

Disease Resistance ◽

Plant Disease Resistance ◽

Molecular Mechanisms ◽

Target Genes ◽

Colletotrichum Gloeosporioides ◽

Juglans Regia ◽

Bioinformatic Analysis ◽

Genome Wide ◽

Phenylpropanoid Biosynthesis ◽

Non Coding Rnas

Abstract Background: Walnut anthracnose caused by Colletotrichum gloeosporioides (Penz.) Penz. and Sacc. is an important walnut production problem in China. Although the long non-coding RNAs (lncRNAs) are important for plant disease resistance , the molecular mechanisms underlying resistance to C. gloeosporioides in walnut remain poorly understood.Results: The anthracnose-resistant F26 fruits from the B26 clone and the anthracnose-susceptible F423 fruits from the 4-23 clone of walnut were used as the test materials. Specifically, we performed a comparative transcriptome analysis of F26 and F423 fruit bracts to identify differentially expressed LncRNAs (DELs) at five time-points (tissues at 0 hpi, pathological tissues at 24 hpi, 48 hpi, 72 hpi, and distal uninoculated tissues at 120 hpi). Compared with F423, a total of 14525 DELs were identified, including 10645 upregulated lncRNAs and 3846 downregulated lncRNAs in F26. The number of upregulated lncRNAs in F26 compared to in F423 was significantly higher at the early stages of C. gloeosporioides infection. A total of 5 modules related to disease resistance were screened by WGCNA and the target genes of lncRNAs were obtained. Bioinformatic analysis showed that the target genes of upregulated lncRNAs were enriched in immune-related processes during the infection of C. gloeosporioides, such as activation of innate immune response, defense response to bacterium, incompatible interaction and immune system process, and enriched in plant hormone signal transduction, phenylpropanoid biosynthesis and other pathways. And 124 known target genes for 96 hub lncRNAs were predicted, including 10 known resistance genes. The expression of 5 lncRNAs and 5 target genes was confirmed by qPCR, which was consistent with the RNA-seq data.Conclusions: The results of this study provide the basis for future functional characterizations of lncRNAs regarding the C. gloeosporioides resistance of walnut fruit bracts.

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Genome-wide identification and expression analysis of the GRAS family proteins in Medicago truncatula

Acta Physiologiae Plantarum ◽

10.1007/s11738-017-2393-x ◽

2017 ◽

Vol 39 (4) ◽

Cited By ~ 11

Author(s):

Lili Song ◽

Lei Tao ◽

Huiping Cui ◽

Lei Ling ◽

Changhong Guo

Keyword(s):

Medicago Truncatula ◽

Expression Analysis ◽

Gras Family ◽

Genome Wide

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Phylogenomics Reveals an Ancient Hybrid Origin of the Persian Walnut

Molecular Biology and Evolution ◽

10.1093/molbev/msz112 ◽

2019 ◽

Vol 36 (11) ◽

pp. 2451-2461 ◽

Cited By ~ 14

Author(s):

Bo-Wen Zhang ◽

Lin-Lin Xu ◽

Nan Li ◽

Peng-Cheng Yan ◽

Xin-Hua Jiang ◽

...

Keyword(s):

Approximate Bayesian Computation ◽

Juglans Regia ◽

Phylogenetic Network ◽

Single Copy ◽

Hybrid Origin ◽

Bayesian Computation ◽

Persian Walnut ◽

Genome Wide ◽

American Black ◽

Approximate Bayesian

Abstract Persian walnut (Juglans regia) is cultivated worldwide for its high-quality wood and nuts, but its origin has remained mysterious because in phylogenies it occupies an unresolved position between American black walnuts and Asian butternuts. Equally unclear is the origin of the only American butternut, J. cinerea. We resequenced the whole genome of 80 individuals from 19 of the 22 species of Juglans and assembled the genome of its relatives Pterocarya stenoptera and Platycarya strobilacea. Using phylogenetic-network analysis of single-copy nuclear genes, genome-wide site pattern probabilities, and Approximate Bayesian Computation, we discovered that J. regia (and its landrace J. sigillata) arose as a hybrid between the American and the Asian lineages and that J. cinerea resulted from massive introgression from an immigrating Asian butternut into the genome of an American black walnut. Approximate Bayesian Computation modeling placed the hybrid origin in the late Pliocene, ∼3.45 My, with both parental lineages since having gone extinct in Europe.

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