scholarly journals Yield is negatively correlated with nucleotide-binding leucine-rich repeat gene content in soybean

2021 ◽  
Author(s):  
Philipp E Bayer ◽  
Haifei Hu ◽  
Jakob Petereit ◽  
Rajeev K Varshney ◽  
Babu Valliyodan ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Seed Weight ◽  
Agronomic Traits ◽  
Significant Negative Correlation ◽  
Gene Content ◽  
Disease Resistance Gene ◽  
R Genes ◽  
Leucine Rich Repeat ◽  
Yield Improvement ◽  
Number Of Genes

The availability of increasing quantities of crop pangenome data permits the detailed association of gene content with agronomic traits. Here, we investigate disease resistance gene content of diverse soybean cultivars and report a significant negative correlation between the number of NLR resistance (R) genes and yield. We find no association between R-genes with seed weight, oil or protein content, and we find no correlation between yield and the number of RLK, RLP genes, or the total number of genes. These results suggest that recent yield improvement in soybean may be partially associated with the selective loss of NLR genes. Three quarters of soybean NLR genes do not show presence/absence variation, limiting the ability to select for their absence, and so the deletion or disabling of select NLR genes may support future yield improvement.

Organization, Expression and Evolution of a Disease Resistance Gene Cluster in Soybean

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 1961-1977
Author(s):  
Michelle A Graham ◽  
Laura Fredrick Marek ◽  
Randy C Shoemaker
Keyword(s):  
Disease Resistance ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Developmental Stages ◽  
Gene Evolution ◽  
Pcr Amplification ◽  
Disease Resistance Genes ◽  
Disease Resistance Gene ◽  
R Genes ◽  
Specific Primers

Abstract PCR amplification was previously used to identify a cluster of resistance gene analogues (RGAs) on soybean linkage group J. Resistance to powdery mildew (Rmd-c), Phytophthora stem and root rot (Rps2), and an ineffective nodulation gene (Rj2) map within this cluster. BAC fingerprinting and RGA-specific primers were used to develop a contig of BAC clones spanning this region in cultivar “Williams 82” [rps2, Rmd (adult onset), rj2]. Two cDNAs with homology to the TIR/NBD/LRR family of R-genes have also been mapped to opposite ends of a BAC in the contig Gm_Isb001_091F11 (BAC 91F11). Sequence analyses of BAC 91F11 identified 16 different resistance-like gene (RLG) sequences with homology to the TIR/NBD/LRR family of disease resistance genes. Four of these RLGs represent two potentially novel classes of disease resistance genes: TIR/NBD domains fused inframe to a putative defense-related protein (NtPRp27-like) and TIR domains fused inframe to soybean calmodulin Ca2+-binding domains. RT-PCR analyses using gene-specific primers allowed us to monitor the expression of individual genes in different tissues and developmental stages. Three genes appeared to be constitutively expressed, while three were differentially expressed. Analyses of the R-genes within this BAC suggest that R-gene evolution in soybean is a complex and dynamic process.

Map-based cloning of a gene sequence encoding a nucleotide-binding domain and a leucine-rich region at the Cre3 nematode resistance locus of wheat

Genome ◽  
1997 ◽  
Vol 40 (5) ◽  
pp. 659-665 ◽  
Author(s):  
Evans S. Lagudah ◽  
Odile Moullet ◽  
Rudi Appels
Keyword(s):  
Disease Resistance ◽  
Gene Family ◽  
Binding Site ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Gene Sequence ◽  
Nucleotide Binding ◽  
Disease Resistance Gene ◽  
Leucine Rich Repeat ◽  
Rich Region

The Cre3 gene confers a high level of resistance to the root endoparasitic nematode Heterodera avenae in wheat. A DNA marker cosegregating with H. avenae resistance was used as an entry point for map-based cloning of a disease resistance gene family at the Cre3 locus. Two related gene sequences have been analysed at the Cre3 locus. One, identified as a cDNA clone, encodes a polypeptide with a nucleotide binding site (NBS) and a leucine-rich region; this member of the disease resistance gene family is expressed in roots. A second Cre3 gene sequence, cloned as genomic DNA, appears to be a pseudogene, with a frame shift caused by a deletion event. These two genes, related to members of the cytoplasmic NBS – leucine rich repeat class of plant disease resistance genes were physically mapped to the distal 0.06 fragment of the long arm of wheat chromosome 2D and cosegregated with nematode resistance.Key words: cereal cyst nematode, disease resistance genes, nucleotide-binding site, leucine-rich repeat.

scholarly journals Bioinformatic-Based Approaches for Disease-Resistance Gene Discovery in Plants

Agronomy ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 2259
Author(s):  
Andrea Fernandez-Gutierrez ◽  
Juan J. Gutierrez-Gonzalez
Keyword(s):  
Disease Resistance ◽  
Resistance Genes ◽  
Gene Annotation ◽  
Pathogen Resistance ◽  
Limiting Factors ◽  
Disease Resistance Gene ◽  
R Genes ◽  
Nucleotide Binding Sites ◽  
Bioinformatic Tools ◽  
Computer Based

Pathogens are among the most limiting factors for crop success and expansion. Thus, finding the underlying genetic cause of pathogen resistance is the main goal for plant geneticists. The activation of a plant’s immune system is mediated by the presence of specific receptors known as disease-resistance genes (R genes). Typical R genes encode functional immune receptors with nucleotide-binding sites (NBS) and leucine-rich repeat (LRR) domains, making the NBS-LRRs the largest family of plant resistance genes. Establishing host resistance is crucial for plant growth and crop yield but also for reducing pesticide use. In this regard, pyramiding R genes is thought to be the most ecologically friendly way to enhance the durability of resistance. To accomplish this, researchers must first identify the related genes, or linked markers, within the genomes. However, the duplicated nature, with the presence of frequent paralogues, and clustered characteristic of NLRs make them difficult to predict with the classic automatic gene annotation pipelines. In the last several years, efforts have been made to develop new methods leading to a proliferation of reports on cloned genes. Herein, we review the bioinformatic tools to assist the discovery of R genes in plants, focusing on well-established pipelines with an important computer-based component.

The Tomato Cf-5 Disease Resistance Gene and Six Homologs Show Pronounced Allelic Variation in Leucine-Rich Repeat Copy Number

1998 ◽  
Vol 10 (11) ◽  
pp. 1915
Author(s):  
Mark S. Dixon ◽  
Kostas Hatzixanthis ◽  
David A. Jones ◽  
Kate Harrison ◽  
Jonathan D. G. Jones
Keyword(s):  
Disease Resistance ◽  
Resistance Gene ◽  
Copy Number ◽  
Allelic Variation ◽  
Disease Resistance Gene ◽  
Leucine Rich Repeat ◽  
Repeat Copy Number ◽  
Repeat Copy

Improvement of multiple agronomic traits by a disease resistance gene via cell wall reinforcement

Nature Plants ◽  
2017 ◽  
Vol 3 (3) ◽  
Author(s):  
Keming Hu ◽  
Jianbo Cao ◽  
Jie Zhang ◽  
Fan Xia ◽  
Yinggen Ke ◽  
...  
Keyword(s):  
Cell Wall ◽  
Disease Resistance ◽  
Resistance Gene ◽  
Agronomic Traits ◽  
Disease Resistance Gene ◽  
Cell Wall Reinforcement

Genetic mapping of plant disease resistance gene homologues using a minimal Brassica napus L. population

Genome ◽  
1999 ◽  
Vol 42 (4) ◽  
pp. 735-743 ◽  
Author(s):  
A Joyeux ◽  
M G Fortin ◽  
R Mayerhofer ◽  
A G Good
Keyword(s):  
Disease Resistance ◽  
Brassica Napus ◽  
Genetic Mapping ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Mapping Population ◽  
Disease Resistance Gene ◽  
Leucine Rich Repeat ◽  
Repeat Domain ◽  
Polymerase Chain

Genetic mapping of plants traditionally involves the analysis of large segregating populations. However, not all individuals in a population contribute equal amounts of genetic information. It is thus possible to achieve rough mapping using a subset of the most informative individuals in the population. We have designed a minimal Brassica napus mapping population of 23 doubled-haploid plants and have tested this method using this population in the mapping of disease resistance gene homologues in B. napus. Several groups have identified such homologues in soybean and potato by amplifying sequences corresponding to conserved nucleotide-binding sites from known resistance genes. However, the sequence conservation in the leucine-rich repeat domain that is present in most of the disease resistance genes isolated has not been exploited via the polymerase chain reaction (PCR). We present the genetic mapping of Brassica napus DNA sequences amplified with primers corresponding to both the nucleotide-binding site and the leucine rich-repeat domain of the Arabidopsis thaliana RPS2 gene. We also describe a method for the quick mapping of resistance gene homologues using the polymerase chain reaction.Key words: Brassica napus, disease resistance genes, minimal mapping population, RFLP markers.

scholarly journals Isolation, Sequence Analysis, and Linkage Mapping of Nucleotide Binding Site–Leucine-rich Repeat Disease Resistance Gene Analogs in Watermelon

2009 ◽  
Vol 134 (6) ◽  
pp. 649-657 ◽  
Author(s):  
Karen R. Harris ◽  
W. Patrick Wechter ◽  
Amnon Levi
Keyword(s):  
Disease Resistance ◽  
Resistance Gene ◽  
Linkage Mapping ◽  
Citrullus Lanatus ◽  
Nucleotide Binding ◽  
Disease Resistance Gene ◽  
Resistance Gene Analogs ◽  
Leucine Rich Repeat ◽  
Degenerate Primers ◽  
Sequence Tagged Sites

Sixty-six watermelon (Citrullus lanatus var. lanatus) disease resistance gene analogs were cloned from ‘Calhoun Gray’, PI 296341, and PI 595203 using degenerate primers to select for the nucleotide binding sites (NBS) from the NBS–leucine-rich repeat (LRR) resistance gene family. After contig assembly, watermelon resistance gene analogs (WRGA) were identified and amino acid sequence alignment revealed that these groups contained motifs characteristic of NBS-LRR resistance genes. Using cluster analysis, eight groups of WRGA were identified and further characterized as having homology to Drosophila Toll and mammalian interleukin-1 receptor (TIR) and non-TIR domains. Three of these WRGA as well as three disease-related watermelon expressed sequence tag homologs were placed on a test-cross map. Linkage mapping placed the WRGA on linkage group XIII, an area on the watermelon map where resistance gene analogs cluster. In addition, these WRGA sequence-tagged sites (STS) were amplified from various genera of the Cucurbitaceae indicating that conservation of resistance gene analogs exists among cucurbits. These WRGA-STS markers may be useful in marker-assisted selection for the improvement for disease resistance in watermelon.

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