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3. Author Response: Characterization of tryptophan oxidation affecting D1 degradation by FtsH in the photosystem II quality control of chloroplasts

Author

Kato, Yusuke, primary, Kuroda, Hiroshi, additional, Ozawa, Shin-Ichiro, additional, Saito, Keisuke, additional, Dogra, Vivek, additional, Scholz, Martin, additional, Zhang, Guoxian, additional, de Vitry, Catherine, additional, Ishikita, Hiroshi, additional, Kim, Chanhong, additional, Hippler, Michael, additional, Takahashi, Yuichiro, additional, and Sakamoto, Wataru, additional

Published
2023
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4. Characterization of tryptophan oxidation affecting D1 degradation by FtsH in the photosystem II quality control of chloroplasts

Author

Kato, Yusuke, primary, Kuroda, Hiroshi, primary, Ozawa, Shin-Ichiro, primary, Saito, Keisuke, additional, Dogra, Vivek, additional, Scholz, Martin, additional, Zhang, Guoxian, additional, de Vitry, Catherine, additional, Ishikita, Hiroshi, additional, Kim, Chanhong, additional, Hippler, Michael, additional, Takahashi, Yuichiro, additional, and Sakamoto, Wataru, additional

Published
2023
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6. Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus Cajan (L.) Millspaugh]

Author

Dutta, Sutapa, Kumawat, Giriraj, Singh, Bikram P, Gupta, Deepak K, Singh, Sangeeta, Dogra, Vivek, Gaikwad, Kishor, Sharma, Tilak R, Raje, Ranjeet S, Bandhopadhya, Tapas K, Datta, Subhojit, Singh, Mahendra N, Bashasab, Fakrudin, Kulwal, Pawan, Wanjari, KB, K Varshney, Rajeev, Cook, Douglas R, and Singh, Nagendra K

Abstract

Abstract Background Pigeonpea [Cajanus cajan (L.) Millspaugh], one of the most important food legumes of semi-arid tropical and subtropical regions, has limited genomic resources, particularly expressed sequence based (genic) markers. We report a comprehensive set of validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing, and its application in genetic diversity analysis and mapping. Results In this study, 43,324 transcriptome shotgun assembly unigene contigs were assembled from 1.696 million 454 GS-FLX sequence reads of separate pooled cDNA libraries prepared from leaf, root, stem and immature seed of two pigeonpea varieties, Asha and UPAS 120. A total of 3,771 genic-SSR loci, excluding homopolymeric and compound repeats, were identified; of which 2,877 PCR primer pairs were designed for marker development. Dinucleotide was the most common repeat motif with a frequency of 60.41%, followed by tri- (34.52%), hexa- (2.62%), tetra- (1.67%) and pentanucleotide (0.76%) repeat motifs. Primers were synthesized and tested for 772 of these loci with repeat lengths of ≥18 bp. Of these, 550 markers were validated for consistent amplification in eight diverse pigeonpea varieties; 71 were found to be polymorphic on agarose gel electrophoresis. Genetic diversity analysis was done on 22 pigeonpea varieties and eight wild species using 20 highly polymorphic genic-SSR markers. The number of alleles at these loci ranged from 4-10 and the polymorphism information content values ranged from 0.46 to 0.72. Neighbor-joining dendrogram showed distinct separation of the different groups of pigeonpea cultivars and wild species. Deep transcriptome sequencing of the two parental lines helped in silico identification of polymorphic genic-SSR loci to facilitate the rapid development of an intra-species reference genetic map, a subset of which was validated for expected allelic segregation in the reference mapping population. Conclusion We developed 550 validated genic-SSR markers in pigeonpea using deep transcriptome sequencing. From these, 20 highly polymorphic markers were used to evaluate the genetic relationship among species of the genus Cajanus. A comprehensive set of genic-SSR markers was developed as an important genomic resource for diversity analysis and genetic mapping in pigeonpea.

Published
2011

20. Seed priming with brassinolides improves growth and reinforces antioxidative defenses under normal and heat stress conditions in seedlings of Brassica juncea.

Author

Neha, Twinkle, Mohapatra, Sumanta, Sirhindi, Geetika, and Dogra, Vivek

Subjects
BRASSICA juncea, YIELD stress, SEEDS, REACTIVE oxygen species, CROP yields, SEEDLINGS
Abstract

Environmental stresses pose a major challenge for plant researchers to fulfill increasing food demand. Researchers are trying to generate high‐yielding and stress‐tolerant or resistant varieties using classical genetics and modern gene‐editing tools; however, both approaches have limitations. Chemical treatments emerged as an alternative to improve yield and impart stress resilience. Brassinosteroids (BRs) are a group of phytohormones that regulate various biological processes, including stress management. With foliar spray methods, BR treatments showed promising results but are not economically feasible. We hypothesize that priming of seeds, which requires lesser amounts of BRs, could be equally effective in promoting growth and stress tolerance. Owing to this notion, we analyzed the impact of priming seeds with selected BRs, namely, 24‐epibrassinolide (EBL) and 28‐homobrassinolide (HBL), in Brassica juncea under normal and heat shock stress conditions. Seeds primed with BRs and grown until seedlings stage at normal conditions (20°C) were subjected to a heat shock (35°C) for a few hours, relating to what plants experience in natural conditions. Heat shock reduced the growth and biomass with an increased accumulation of reactive oxygen species. As anticipated, BRs treatments significantly improved the growth and physiological parameters with an enhanced antioxidant defense under both conditions. Transcriptional analyses revealed that BRs concomitantly induce growth and oxidative stress‐responsive gene expression via the canonical BR‐signaling pathway. Transfer of unstressed and heat‐shock‐treated seedlings to field conditions demonstrated the long‐term effectivity of BR‐priming. Our results showed seed priming with BRs could improve growth and resilience against heat shock; hence, it appears to be a viable strategy to enhance crop yields and stress tolerance. [ABSTRACT FROM AUTHOR]

Published
2022
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22. Plant proteomics in India and Nepal: current status and challenges ahead

Author

Deswal, Renu, Gupta, Ravi, Dogra, Vivek, Singh, Raksha, Abat, Jasmeet Kaur, Sarkar, Abhijit, Mishra, Yogesh, Rai, Vandana, Sreenivasulu, Yelam, Amalraj, Ramesh Sundar, Raorane, Manish, Chaudhary, Ram Prasad, Kohli, Ajay, Giri, Ashok Prabhakar, Chakraborty, Niranjan, Zargar, Sajad Majeed, Agrawal, Vishwanath Prasad, Agrawal, Ganesh Kumar, Job, Dominique, Renaut, Jenny, and Rakwal, Randeep

Published
2013
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24. The first draft of the pigeonpea genome sequence

Author

Singh, Nagendra K., Gupta, Deepak K., Jayaswal, Pawan K., Mahato, Ajay K., Dutta, Sutapa, Singh, Sangeeta, Bhutani, Shefali, Dogra, Vivek, Singh, Bikram P., Kumawat, Giriraj, Pal, Jitendra K., Pandit, Awadhesh, Singh, Archana, Rawal, Hukum, Kumar, Akhilesh, Rama Prashat, G., Khare, Ambika, Yadav, Rekha, Raje, Ranjit S., Singh, Mahendra N., Datta, Subhojit, Fakrudin, Bashasab, Wanjari, Keshav B., Kansal, Rekha, Dash, Prasanta K., Jain, Pradeep K., Bhattacharya, Ramcharan, Gaikwad, Kishor, Mohapatra, Trilochan, Srinivasan, R., and Sharma, Tilak R.

Published
2012
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26. Antagonistic modules, SIB1 and LSD1, regulate photosynthesis-associated nuclear genes via GOLDEN2-LIKE transcription factors in Arabidopsis

Author

Tong Liu, Keun Pyo Lee, Weiman Xing, Chanhong Kim, Dogra Vivek, Jianli Duan, Mengping Li, and Mengshuang Li

Subjects
biology, Chemistry, Arabidopsis, Regulator, Retrograde signaling, Promoter, Transcription coregulator, biology.organism_classification, Chromatin immunoprecipitation, Transcription factor, Biogenesis, Cell biology
Abstract

GOLDEN2-LIKE (GLK) transcription factors drive the expression of photosynthesis-associated nuclear genes (PhANGs), indispensable for chloroplast biogenesis. We previously demonstrated that the salicylic acid (SA)-induced SIGMA FACTOR-BINDING PROTEIN 1 (SIB1), a transcription coregulator and positive regulator of cell death, interacts with GLK1 and GLK2 to reinforce their activities. The SIB1-GLK interaction raises the level of light-harvesting antenna proteins in photosystem II, aggravating photoinhibition and singlet oxygen (1O2) burst. 1O2 then contributes to SA-induced cell death via EXECUTER 1 (EX1, 1O2 sensor protein)-mediated retrograde signaling upon reaching a critical level. We now reveal that LESION-SIMULATING DISEASE 1 (LSD1), a transcription coregulator and negative regulator of SA-primed cell death, interacts with GLK1/2 to repress their activities. Consistently, the overexpression of LSD1 represses GLK target genes including PhANGs, whereas the loss of LSD1 increases their expression. Remarkably, LSD1 overexpression inhibits chloroplast biogenesis, resembling the characteristic glk1glk2 double mutant phenotype. The subsequent chromatin immunoprecipitation analysis coupled with quantitative PCR further reveals that LSD1 inhibits the DNA-binding activity of GLK1 towards its target promoters. The SA-induced nuclear-targeted SIB1 appears to counteractively interact with GLK1/2, leading to the activation of EX1-mediated 1O2 signaling. Taken together, we provide a working model that SIB1 and LSD1, mutually exclusive SA-signaling components, antagonistically regulate GLK1/2 to fine-tune the expression of PhANGs, thereby modulating 1O2 homeostasis and related stress responses.

Published
2020

29. TIC236 gain-of-function mutations unveil the link between plastid division and plastid protein import.

Author

Jun Fang, Bingqi Li, Lih-Jen Chen, Dogra, Vivek, Shengji Luo, Wangpin Wu, Pengcheng Wang, Inhwan Hwang, Hsou-min Li, and Chanhong Kim

Subjects
GAIN-of-function mutations, UBIQUITIN ligases, MEMBRANE proteins, CHLOROPLAST membranes, GENETIC testing, COMMERCIAL products
Abstract

TIC236 is an essential component of the translocon for protein import into chloroplasts, as evidenced by the embryonic lethality of the knockout mutant. Here, we unveil a TIC236-allied component, the chloroplast outer membrane protein CRUMPLED LEAF (CRL), absence of which impairs plastid division and induces autoimmune responses in Arabidopsis thaliana. A forward genetic screen exploring CRL function found multiple dominant TIC236 gain-of-function (tic236-gf) mutations that abolished crl-induced phenotypes. Moreover, CRL associates with TIC236, and a tic236-knockdown mutant exhibited multiple lesions similar to the crl mutant, supporting their shared functionality. Consistent with the defective plastid division phenotype of crl, CRL interacts with the transit peptides of proteins essential in plastid division, with tic236-gf mutations reinforcing their import via increased TIC236 stability. Ensuing reverse genetic analyses further revealed genetic interaction between CRL and SP1, a RING-type ubiquitin E3 ligase, as well as with the plastid protease FTSH11, which function in TOC and TIC protein turnover, respectively. Loss of either SP1 or FTSH11 rescued crl mutant phenotypes to varying degrees due to increased translocon levels. Collectively, our data shed light on the links between plastid protein import, plastid division, and plant stress responses. [ABSTRACT FROM AUTHOR]

Published
2022
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30. The tomato genome sequence provides insights into fleshy fruit evolution

Author

Sato, Shusei, Tabata, Satoshi, Hirakawa, Hideki, Asamizu, Erika, Shirasawa, Kenta, Isobe, Sachiko, Kaneko, Takakazu, Nakamura, Yasukazu, Shibata, Daisuke, Aoki, Koh, Egholm, Michael, Knight, James, Bogden, Robert, Li, Changbao, Shuang, Yang, Xu, Xun, Pan, Shengkai, Cheng, Shifeng, Liu, Xin, Ren, Yuanyuan, Wang, Jun, Albiero, Alessandro, Dal Pero, Francesca, Todesco, Sara, Van Eck, Joyce, Buels, Robert M., Bombarely, Aureliano, Gosselin, Joseph R., Huang, Minyun, Leto, Jonathan A., Menda, Naama, Strickler, Susan, Mao, Linyong, Gao, Shan, Tecle, Isaak Y., York, Thomas, Zheng, Yi, Vrebalov, Julia T., Lee, JeMin, Zhong, Silin, Mueller, Lukas A., Stiekema, Willem J., Ribeca, Paolo, Alioto, Tyler, Yang, Wencai, Huang, Sanwen, Du, Yongchen, Zhang, Zhonghua, Gao, Jianchang, Guo, Yanmei, Wang, Xiaoxuan, Li, Ying, He, Jun, Li, Chuanyou, Cheng, Zhukuan, Zuo, Jianru, Ren, Jianfeng, Zhao, Jiuhai, Yan, Liuhua, Jiang, Hongling, Wang, Bao, Li, Hongshuang, Li, Zhenjun, Fu, Fuyou, Chen, Bingtang, Han, Bin, Feng, Qi, Fan, Danlin, Wang, Ying, Ling, Hongqing, Xue, Yongbiao, Ware, Doreen, Richard McCombie, W., Lippman, Zachary B., Chia, Jer-Ming, Jiang, Ke, Pasternak, Shiran, Gelley, Laura, Kramer, Melissa, Anderson, Lorinda K., Chang, Song-Bin, Royer, Suzanne M., Shearer, Lindsay A., Stack, Stephen M., Rose, Jocelyn K. C., Xu, Yimin, Eannetta, Nancy, Matas, Antonio J., McQuinn, Ryan, Tanksley, Steven D., Camara, Francisco, Guigó, Roderic, Rombauts, Stephane, Fawcett, Jeffrey, Van de Peer, Yves, Zamir, Dani, Liang, Chunbo, Spannagl, Manuel, Gundlach, Heidrun, Bruggmann, Remy, Mayer, Klaus, Jia, Zhiqi, Zhang, Junhong, Ye, Zhibiao, Bishop, Gerard J., Butcher, Sarah, Lopez-Cobollo, Rosa, Buchan, Daniel, Filippis, Ioannis, Abbott, James, Dixit, Rekha, Singh, Manju, Singh, Archana, Kumar Pal, Jitendra, Pandit, Awadhesh, Kumar Singh, Pradeep, Kumar Mahato, Ajay, Dogra, Vivek, Gaikwad, Kishor, Raj Sharma, Tilak, Mohapatra, Trilochan, Kumar Singh, Nagendra, Causse, Mathilde, Rothan, Christophe, Schiex, Thomas, Noirot, Céline, Bellec, Arnaud, Klopp, Christophe, Delalande, Corinne, Berges, Hélène, Mariette, Jérôme, Frasse, Pierre, Vautrin, Sonia, Zouine, Mohamed, Latché, Alain, Rousseau, Christine, Regad, Farid, Pech, Jean-Claude, Philippot, Murielle, Bouzayen, Mondher, Pericard, Pierre, Osorio, Sonia, Fernandez del Carmen, Asunción, Monforte, Antonio, Granell, Antonio, Fernandez-Muñoz, Rafael, Conte, Mariana, Lichtenstein, Gabriel, Carrari, Fernando, De Bellis, Gianluca, Fuligni, Fabio, Peano, Clelia, Grandillo, Silvana, Termolino, Pasquale, Pietrella, Marco, Fantini, Elio, Falcone, Giulia, Fiore, Alessia, Giuliano, Giovanni, Lopez, Loredana, Facella, Paolo, Perrotta, Gaetano, Daddiego, Loretta, Bryan, Glenn, Orozco, Modesto, Pastor, Xavier, Torrents, David, van Schriek, Marco G. M., Feron, Richard M.C., van Oeveren, Jan, de Heer, Peter, daPonte, Lorena, Jacobs-Oomen, Saskia, Cariaso, Mike, Prins, Marcel, van Eijk, Michiel J. T., Janssen, Antoine, van Haaren, Mark J. J., Jo, Sung-Hwan, Kim, Jungeun, Kwon, Suk-Yoon, Kim, Sangmi, Koo, Dal-Hoe, Lee, Sanghyeob, Hur, Cheol-Goo, Clouser, Christopher, Rico, Alain, Hallab, Asis, Gebhardt, Christiane, Klee, Kathrin, Jöcker, Anika, Warfsmann, Jens, Göbel, Ulrike, Kawamura, Shingo, Yano, Kentaro, Sherman, Jamie D., Fukuoka, Hiroyuki, Negoro, Satomi, Bhutty, Sarita, Chowdhury, Parul, Chattopadhyay, Debasis, Datema, Erwin, Smit, Sandra, Schijlen, Elio G. W. M., van de Belt, Jose, van Haarst, Jan C., Peters, Sander A., van Staveren, Marjo J., Henkens, Marleen H. C., Mooyman, Paul J. W., Hesselink, Thamara, van Ham, Roeland C. H. J., Jiang, Guoyong, Droege, Marcus, Choi, Doil, Kang, Byung-Cheol, Dong Kim, Byung, Park, Minkyu, Kim, Seungill, Yeom, Seon-In, Lee, Yong-Hwan, Choi, Yang-Do, Li, Guangcun, Gao, Jianwei, Liu, Yongsheng, Huang, Shengxiong, Fernandez-Pedrosa, Victoria, Collado, Carmen, Zuñiga, Sheila, Wang, Guoping, Cade, Rebecca, Dietrich, Robert A., Rogers, Jane, Knapp, Sandra, Fei, Zhangjun, White, Ruth A., Thannhauser, Theodore W., Giovannoni, James J., Angel Botella, Miguel, Gilbert, Louise, Gonzalez, Ramon, Luis Goicoechea, Jose, Yu, Yeisoo, Kudrna, David, Collura, Kristi, Wissotski, Marina, Wing, Rod, Schoof, Heiko, Meyers, Blake C., Bala Gurazada, Aishwarya, Green, Pamela J., Mathur, Saloni, Vyas, Shailendra, Solanke, Amolkumar U., Kumar, Rahul, Gupta, Vikrant, Sharma, Arun K., Khurana, Paramjit, Khurana, Jitendra P., Tyagi, Akhilesh K., Dalmay, Tamas, Mohorianu, Irina, Walts, Brandon, Chamala, Srikar, Brad Barbazuk, W., Li, Jingping, Guo, Hui, Lee, Tae-Ho, Wang, Yupeng, Zhang, Dong, Paterson, Andrew H., Wang, Xiyin, Tang, Haibao, Barone, Amalia, Luisa Chiusano, Maria, Raffaella Ercolano, Maria, D’Agostino, Nunzio, Di Filippo, Miriam, Traini, Alessandra, Sanseverino, Walter, Frusciante, Luigi, Seymour, Graham B., Elharam, Mounir, Fu, Ying, Hua, Axin, Kenton, Steven, Lewis, Jennifer, Lin, Shaoping, Najar, Fares, Lai, Hongshing, Qin, Baifang, Qu, Chunmei, Shi, Ruihua, White, Douglas, White, James, Xing, Yanbo, Yang, Keqin, Yi, Jing, Yao, Ziyun, Zhou, Liping, Roe, Bruce A., Vezzi, Alessandro, D’Angelo, Michela, Zimbello, Rosanna, Schiavon, Riccardo, Caniato, Elisa, Rigobello, Chiara, Campagna, Davide, Vitulo, Nicola, Valle, Giorgio, Nelson, David R., De Paoli, Emanuele, Szinay, Dora, de Jong, Hans H., Bai, Yuling, Visser, Richard G. F., Klein Lankhorst, René M., Beasley, Helen, McLaren, Karen, Nicholson, Christine, Riddle, Claire, and Gianese, Giulio

Published
2012
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31. The Arabidopsis CRUMPLED LEAF protein, a homolog of the cyanobacterial bilin lyase, retains the bilin‐binding pocket for a yet unknown function

Author

Wang, Fangfang, primary, Fang, Jun, additional, Guan, Kaoling, additional, Luo, Shengji, additional, Dogra, Vivek, additional, Li, Bingqi, additional, Ma, Demin, additional, Zhao, Xinyan, additional, Lee, Keun Pyo, additional, Sun, Pengkai, additional, Xin, Jian, additional, Liu, Tong, additional, Xing, Weiman, additional, and Kim, Chanhong, additional

Published
2020
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34. PLANT NATRIURETIC PEPTIDE A and Its Putative Receptor PNP-R2 Antagonize Salicylic Acid–Mediated Signaling and Cell Death

Author

Lee, Keun Pyo, primary, Liu, Kaiwei, additional, Kim, Eun Yu, additional, Medina-Puche, Laura, additional, Dong, Haihong, additional, Duan, Jianli, additional, Li, Mengping, additional, Dogra, Vivek, additional, Li, Yingrui, additional, Lv, Ruiqing, additional, Li, Zihao, additional, Lozano-Duran, Rosa, additional, and Kim, Chanhong, additional

Published
2020
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41. Singlet oxygen-triggered chloroplast-to-nucleus retrograde signalling pathways: an emerging perspective

Author

Dogra, Vivek, Rochaix, Jean-David, and Kim, Chanhong

Subjects
Oxygen, Singlet, ddc:580, ddc:570, β-carotene, Photoinhibition, Retrograde signalling, food and beverages, Acclimation, EXECUTER1, Programmed cell death
Abstract

Singlet oxygen (¹O₂) is a prime cause of photo-damage of the photosynthetic apparatus. The chlorophyll molecules in the photosystem II reaction center and in the light-harvesting antenna complex are major sources of ¹O₂ generation. It has been thought that the generation of ¹O₂ mainly takes place in the appressed regions of the thylakoid membranes, namely, the grana core, where most of the active photosystem II complexes are localized. Apart from being a toxic molecule, new evidence suggests that ¹O₂ significantly contributes to chloroplast-to-nucleus retrograde signalling that primes acclimation and cell death responses. Interestingly, recent studies reveal that chloroplasts operate two distinct ¹O₂-triggered retrograde signalling pathways in which β-carotene and a nuclear-encoded chloroplast protein EXECUTER1 play essential roles as signalling mediators. The coexistence of these mediators raises several questions: their crosstalk, source(s) of ¹O₂, downstream signalling components, and the perception and reaction mechanism of these mediators towards ¹O₂. In this review, we mainly discuss the molecular genetic basis of the mode of action of these two putative ¹O₂ sensors and their corresponding retrograde signalling pathways. In addition, we also propose the possible existence of an alternative source of ¹O₂, which is spatially and functionally separated from the grana core.

Published
2018

43. Impaired PSII Proteostasis Promotes Retrograde Signaling via Salicylic Acid

Author

Duan, Jianli, primary, Lee, Keun Pyo, additional, Dogra, Vivek, additional, Zhang, Siyuan, additional, Liu, Kaiwei, additional, Caceres-Moreno, Carlos, additional, Lv, Shanshan, additional, Xing, Weiman, additional, Kato, Yusuke, additional, Sakamoto, Wataru, additional, Liu, Renyi, additional, Macho, Alberto P., additional, and Kim, Chanhong, additional

Published
2019
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46. Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh]

Author

Bashasab Fakrudin, Singh Mahendra N, Datta Subhojit, Bandhopadhya Tapas K, Raje Ranjeet S, Sharma Tilak R, Gaikwad Kishor, Dogra Vivek, Singh Sangeeta, Gupta Deepak K, Singh Bikram P, Kumawat Giriraj, Dutta Sutapa, Kulwal Pawan, Wanjari KB, K Varshney Rajeev, Cook Douglas R, and Singh Nagendra K

Subjects
Botany, QK1-989
Abstract

Abstract Background Pigeonpea [Cajanus cajan (L.) Millspaugh], one of the most important food legumes of semi-arid tropical and subtropical regions, has limited genomic resources, particularly expressed sequence based (genic) markers. We report a comprehensive set of validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing, and its application in genetic diversity analysis and mapping. Results In this study, 43,324 transcriptome shotgun assembly unigene contigs were assembled from 1.696 million 454 GS-FLX sequence reads of separate pooled cDNA libraries prepared from leaf, root, stem and immature seed of two pigeonpea varieties, Asha and UPAS 120. A total of 3,771 genic-SSR loci, excluding homopolymeric and compound repeats, were identified; of which 2,877 PCR primer pairs were designed for marker development. Dinucleotide was the most common repeat motif with a frequency of 60.41%, followed by tri- (34.52%), hexa- (2.62%), tetra- (1.67%) and pentanucleotide (0.76%) repeat motifs. Primers were synthesized and tested for 772 of these loci with repeat lengths of ≥18 bp. Of these, 550 markers were validated for consistent amplification in eight diverse pigeonpea varieties; 71 were found to be polymorphic on agarose gel electrophoresis. Genetic diversity analysis was done on 22 pigeonpea varieties and eight wild species using 20 highly polymorphic genic-SSR markers. The number of alleles at these loci ranged from 4-10 and the polymorphism information content values ranged from 0.46 to 0.72. Neighbor-joining dendrogram showed distinct separation of the different groups of pigeonpea cultivars and wild species. Deep transcriptome sequencing of the two parental lines helped in silico identification of polymorphic genic-SSR loci to facilitate the rapid development of an intra-species reference genetic map, a subset of which was validated for expected allelic segregation in the reference mapping population. Conclusion We developed 550 validated genic-SSR markers in pigeonpea using deep transcriptome sequencing. From these, 20 highly polymorphic markers were used to evaluate the genetic relationship among species of the genus Cajanus. A comprehensive set of genic-SSR markers was developed as an important genomic resource for diversity analysis and genetic mapping in pigeonpea.

Published
2011
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