Gene divergence of homeologous regions associated with a major seed protein content QTL in soybean

Lestari, Puji; Van, Kyujung; Lee, Jay Ern; Kang, Yang Jae; Lee, Suk-Ha

doi:10.3389/fpls.2013.00176

Cited by 28 publications

(29 citation statements)

References 43 publications

(63 reference statements)

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“…Recent genome duplication also revealed homologous retention and chromosomal rearrangement (Schmuts et al, 2010). Homeologous blocks such as QTLs related to protein and oil content along with the corresponding genes have been identified in duplicated segments on the twenty chromosomes of soybean genome as depicted in Figure 1A (Lestari et al, 2013). DNA-based transposed duplications are enriched in disease resistance gene homologs in A. thaliana ( Figure 1B) and WGS duplications are enriched in the C 2 H 2 zinc finger protein in rice ( Figure 1C).…”

Section: Genome and Gene Duplications In Plantsmentioning

confidence: 99%

“…Furthermore, some logic hypothesis propose that fixed gene duplication playing an adaptive role in dosage response to environmental stresses are thought to be the functions of gene duplication with characterized adaptive roles (Flagel and Wendel, 2009). It is also instructive to predict the gene categories/types (Lestari et al, 2013), B = disease resistance gene homologs in A. thalilana (Wang et al, 2011), C = C2H2 zinc finger gene family in rice (Wang et al, 2011). Chr1-Chr20, AT1-AT5, and OS1-OS12 in each circus denote the shown chromosome number of the corresponding plant genomes.…”

Section: Gene Duplication As An Adaptation Mechanismmentioning

confidence: 99%

“…Well predicted QTLs and candidate genes for stress tolerance may reveal novel mechanism of adaptation in soybean . As a result of recent genome duplication, gene duplication could contribute not only to environmental adaptation but also affect other agronomical important traits in soybean such as seed protein/oil content Lestari et al, 2013). …”

Section: A B Cmentioning

confidence: 99%

“…Synteny blocks consisting of QTLs responsible for bruchid resistance matched soybean synteny blocks locating SSR markers associated with nematode resistance QTLs . More than 1100 QTLs and 60,000 protein-coding loci are beneficial to reveal stress-response genes, which have been built into soybean databases (www.phytozome.net/soybean; http://soybase.org) and elucidated for their syntenies within duplication regions in soybean and with other legumes (Kang et al, 2012(Kang et al, , 2014(Kang et al, , 2015Kim et al, 2015;Lestari et al, 2013). Syntenic QTL regions have been detected between chromosome pairs in soybean genome, showing duplicated genes clustered in homeologous QTLs to be possibly associated with environmental specific regulation as demonstrated in chromosomes 6 and 13 .…”

Section: Prospects and Challenges On The Application Of Gene Duplicatmentioning

confidence: 99%

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Gene Duplication to Reveal Adaptation Clue of Plant to Environmental Stress: A Case Study of NBS-LRR Genes in Soybean

Lestari¹,

Lee²,

Tasma³

et al. 2018

J. AgroBiogen

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ABSTRAK Gen responsif terhadap cekaman lingkungan yang bertahan setelah mengalami duplikasi genom skala kecil merupakan bagian dari duplikasi genom. Namun demikian, informasi duplikasi gen yang berpengaruh terhadap sifat adaptif tanaman terhadap perubahan lingkungan masih terbatas. Ulasan ini menyajikan gambaran peristiwa duplikasi dalam genom tanaman yang berdampak terhadap duplikasi gen yang berkaitan dengan perubahan lingkungan, informasi duplikasi gen yang merupakan bagian dari mekanisme adaptasi, kasus duplikasi gen nucleotide-binding site-leucine-rich repeat (NBS-LRR) pada kedelai, dan implementasi informasi duplikasi gen terhadap pemuliaan kedelai di Indonesia. Peristiwa duplikasi genom menghasilkan duplikasi gen dan berperan terhadap evolusi adaptasi pada perubahan lingkungan. Informasi umum tentang tanaman yang beradaptasi dengan cekaman lingkungan memungkinkan untuk meningkatkan pemahaman kita tentang duplikasi gen sebagai mekanisme adaptasi. Gen-gen NBS-LRR yang terduplikasi diketahui berasosiasi dengan QTL terkait ketahanan penyakit dan ekspresi diferensialnya membuktikan kontribusi gen tersebut pada ketahanan kedelai terhadap cekaman biotik. Model yang diusulkan dari proses gen duplikasi NBS-LRR dapat membantu dalam memahami respons gen tersebut terhadap perubahan lingkungan. Duplikasi gen ketahanan terhadap hama/penyakit, NBS-LRR khususnya, memberikan informasi penting dalam pemilihan tetua pemuliaan dan pengembangan marka molekuler terkait ketahanan penyakit untuk memperbaiki kedelai di Indonesia secara genetik. Karena itu, sangat mungkin untuk meningkatkan program pemuliaan yang menargetkan gen ketahanan terhadap cekaman biotik/abiotik dan memberikan dasar molekuler sebagai strategi perlindungan tanaman terhadap cekaman dan pengembangan kultivar kedelai khusus untuk lingkungan ekstrim.Kata kunci: Cekaman lingkungan, duplikasi gen, hama/penyakit, kedelai, NBS-LRR.

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Section: Genome and Gene Duplications In Plantsmentioning

confidence: 99%

Section: Gene Duplication As An Adaptation Mechanismmentioning

confidence: 99%

Section: A B Cmentioning

confidence: 99%

Section: Prospects and Challenges On The Application Of Gene Duplicatmentioning

confidence: 99%

See 2 more Smart Citations

Gene Duplication to Reveal Adaptation Clue of Plant to Environmental Stress: A Case Study of NBS-LRR Genes in Soybean

Lestari¹,

Lee²,

Tasma³

et al. 2018

J. AgroBiogen

Self Cite

View full text Add to dashboard Cite

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“…This is also seen by (Lestari et al, 2013) showing that the major QTL for soybean seed protein and oil in Chr20 had duplicated homeologous regions in Chr10 that occurred due to duplication event. Therefore, the primary and homeologous QTL intervals on different chromosomes might result from genome duplication and then undergo rapid divergence and reorganization.…”

Section: Co-localization and Association Of Nbs-lrr Genes And Qtl Intmentioning

confidence: 74%

Genome wide identification of NBS-LRR genes in Brassica and their association with disease resistance in Brassica napus

Alamery¹

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Brassica napus (canola/rapeseed/oilseed rape) is an important commercial oilseed crop in Australia with an annual production of approximately 1.6 million tons of oil. Canola is an important source of edible vegetable oil and has a broad range of industrial purposes. Blackleg disease (stem canker) caused by the fungal pathogen Leptosphaeria maculans, is one of the most devastating diseases in B. napus. This disease causes significant yield losses with an annual average loss of 15 to 48 %, although losses can reach up to 80% worldwide, mainly in Europe, Australia and Canada.In order to develop an effective strategy to control the blackleg disease, there is a need to identify blackleg resistance genes in Brassica species and understand the genetic interaction between plant resistance genes and the pathogen avirulence genes. Thus, identification of Nucleotide Binding SiteLeucine Rich Repeat (NBS-LRR) resistance genes is one of the most important objectives of understanding resistance. NBS-LRR resistance genes have been extensively studied because they represent the largest class of disease resistance genes and play a critical role in defending plants from pathogens.The objective of this study was to perform comprehensive analysis on identification and characterization of NBS-LRR genes in the B. napus genome and to study the synteny and conservation of NBS-LRR genes between Brassica species. In this study, a total of 641, 249 and 443 NBS-LRR encoding genes in B. napus, B. rapa and B. oleracea, respectively, were identified.The comparative analysis between B. napus and its progenitor species indicated that NBS-LRR genes exhibited similar gene structure, genomic location, arrangement in clusters and syntenic relationships. The results provide evidence that there was a selective advantage to maintaining similar features of NBS-LRR genes in B. napus to both B. rapa and B. oleracea following polyploidization. More than 60% of NBS LRR genes from the progenitor species were conserved.The differences in NBS-LRR gene conservation could be attributed to gene losses or selection pressure to offer species-specific or cultivars-specific resistance.This study found that the NBS-LRR resistance genes are physically clustered and individual genes involved in clusters were more polymorphic and subject to evolutionary process than singleton genes. These clusters, which have been described in many other species, provide a reservoir of genetic variation influenced by tandem duplication and selection pressure. In addition, there was a significant correlation and co-localization between the number of NBS-LRR genes within the disease QTL intervals and the number of genes involved in gene clusters or duplication. This ii correlation provides evidence that NBS-LRR are distributed and clustered throughout the genome and tends to be linked and associated with disease QTL intervals. Chalhoub, B., Denoeud, F., Liu, S., Parkin, I. A. P., Tang, H., Wang, X., Chiquet, J., Belcram, H., Tong, C., Samans, B., Corréa, M., Da Silva, C., Just, ...

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Molecular mapping and genomics of soybean seed protein: a review and perspective for the future

et al. 2017

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Key message Genetic improvement of soybean protein meal is a complex process because of negative correlation with oil, yield, and temperature. This review describes the progress in mapping and genomics, identifies knowledge gaps, and highlights the need of integrated approaches. AbstractMeal protein derived from soybean [Glycine max (L) Merr.] seed is the primary source of protein in poultry and livestock feed. Protein is a key factor that determines the nutritional and economical value of soybean. Genetic improvement of soybean seed protein content is highly desirable, and major quantitative trait loci (QTL) for soybean protein have been detected and repeatedly mapped on chromosomes (Chr.) 20 (LG-I), and 15 (LG-E). However, practical breeding progress is challenging because of seed protein content’s negative genetic correlation with seed yield, other seed components such as oil and sucrose, and interaction with environmental effects such as temperature during seed development. In this review, we discuss rate-limiting factors related to soybean protein content and nutritional quality, and potential control factors regulating seed storage protein. In addition, we describe advances in next-generation sequencing technologies for precise detection of natural variants and their integration with conventional and high-throughput genotyping technologies. A syntenic analysis of QTL on Chr. 15 and 20 was performed. Finally, we discuss comprehensive approaches for integrating protein and amino acid QTL, genome-wide association studies, whole-genome resequencing, and transcriptome data to accelerate identification of genomic hot spots for allele introgression and soybean meal protein improvement.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-017-2955-8) contains supplementary material, which is available to authorized users.

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Gene divergence of homeologous regions associated with a major seed protein content QTL in soybean

Cited by 28 publications

References 43 publications

Gene Duplication to Reveal Adaptation Clue of Plant to Environmental Stress: A Case Study of NBS-LRR Genes in Soybean

Gene Duplication to Reveal Adaptation Clue of Plant to Environmental Stress: A Case Study of NBS-LRR Genes in Soybean

Genome wide identification of NBS-LRR genes in Brassica and their association with disease resistance in Brassica napus

Molecular mapping and genomics of soybean seed protein: a review and perspective for the future

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