MutMap Approach Enables Rapid Identification of Candidate Genes and Development of Markers Associated With Early Flowering and Enhanced Seed Size in Chickpea (Cicer arietinum L.)

Article

Manchikatla, Praveen Kumar, Kalavikatte, Danamma, Mallikarjuna, Bingi Pujari, Palakurthi, Ramesh, Khan, Aamir W., Jha, Uday Chand, Bajaj, Prasad, Singam, Prashant, Chitikineni, Annapurna, Varshney, Rajeev K. and Thudi, Mahandar. 2021. "MutMap Approach Enables Rapid Identification of Candidate Genes and Development of Markers Associated With Early Flowering and Enhanced Seed Size in Chickpea (Cicer arietinum L.)." Frontiers in Plant Science. 12, pp. 1-11. https://doi.org/10.3389/fpls.2021.688694
Article Title

MutMap Approach Enables Rapid Identification of Candidate Genes and Development of Markers Associated With Early Flowering and Enhanced Seed Size in Chickpea (Cicer arietinum L.)

ERA Journal ID200524
Article CategoryArticle
AuthorsManchikatla, Praveen Kumar (Author), Kalavikatte, Danamma (Author), Mallikarjuna, Bingi Pujari (Author), Palakurthi, Ramesh (Author), Khan, Aamir W. (Author), Jha, Uday Chand (Author), Bajaj, Prasad (Author), Singam, Prashant (Author), Chitikineni, Annapurna (Author), Varshney, Rajeev K. (Author) and Thudi, Mahandar (Author)
Journal TitleFrontiers in Plant Science
Journal Citation12, pp. 1-11
Article Number688694
Number of Pages11
Year2021
PublisherFrontiers Media SA
Place of PublicationSwitzerland
ISSN1664-462X
Digital Object Identifier (DOI)https://doi.org/10.3389/fpls.2021.688694
Web Address (URL)https://www.frontiersin.org/articles/10.3389/fpls.2021.688694/full
Abstract

Globally terminal drought is one of the major constraints to chickpea (Cicer arietinum L.) production. Early flowering genotypes escape terminal drought, and the increase in seed size compensates for yield losses arising from terminal drought. A MutMap population for early flowering and large seed size was developed by crossing the mutant line ICC4958-M3-2828 with wild-type ICC 4958. Based on the phenotyping of MutMap population, extreme bulks for days to flowering and 100-seed weight were sequenced using Hi-Seq2500 at 10X coverage. On aligning 47.41 million filtered reads to the CDC Frontier reference genome, 31.41 million reads were mapped and 332,395 single nucleotide polymorphisms (SNPs) were called. A reference genome assembly for ICC 4958 was developed replacing these SNPs in particular positions of the CDC Frontier genome. SNPs specific for each mutant bulk ranged from 3,993 to 5,771. We report a single unique genomic region on Ca6 (between 9.76 and 12.96 Mb) harboring 31, 22, 17, and 32 SNPs with a peak of SNP index = 1 for low bulk for flowering time, high bulk for flowering time, high bulk for 100-seed weight, and low bulk for 100-seed weight, respectively. Among these, 22 SNPs are present in 20 candidate genes and had a moderate allelic impact on the genes. Two markers, Ca6EF10509893 for early flowering and Ca6HSDW10099486 for 100-seed weight, were developed and validated using the candidate SNPs. Thus, the associated genes, candidate SNPs, and markers developed in this study are useful for breeding chickpea varieties that mitigate yield losses under drought stress.

Keywords100 seed weight; candidate genes and SNPs; chickpea; early flowering; MutMap
ANZSRC Field of Research 2020300406. Crop and pasture improvement (incl. selection and breeding)
Institution of OriginUniversity of Southern Queensland
Byline AffiliationsInternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT), India
Indian Council of Agricultural Research, India
Osmania University, India
Centre for Crop Health
Permalink -

https://research.usq.edu.au/item/q6y45/mutmap-approach-enables-rapid-identification-of-candidate-genes-and-development-of-markers-associated-with-early-flowering-and-enhanced-seed-size-in-chickpea-cicer-arietinum-l

Log in to edit

Download files

Published Version
MutMap Approach Enables Rapid Identification of Candidate Genes and Development of Markers Associated With Early Flowering and Enhanced Seed Size in Chickpea (Cicer arietinum L.).pdf
License: CC BY 4.0
File access level: Anyone

  • 78
    total views
  • 52
    total downloads
  • 4
    views this month
  • 2
    downloads this month

Export as

Related outputs

Genome-wide association mapping reveals novel genes and genomic regions controlling root-lesion nematode resistance in chickpea mini core collection
Kumar, Ashish, Naik, Yogesh Dashrath, Gautam, Vedant, Patil, Sunanda, Valluri, Vinod, Channale, Sonal, Bhatt, Jayant, Sharma, Stuti, Ramakrishnan, R. S., Sharma, Radheshyam, Kudapa, Himabindu, Zwart, Rebecca S., Punnuri, Somashekhar M., Varshney, Rajeev K. and Thudi, Mahendar. 2024. "Genome-wide association mapping reveals novel genes and genomic regions controlling root-lesion nematode resistance in chickpea mini core collection." The Plant Genome. https://doi.org/10.1002/tpg2.20508
Development and evaluation of Fusarium wilt-resistant and high-yielding chickpea advanced breeding line, KCD 11
Laxuman, C., Naik, Yogesh Dashrath, Desai, B. K., Kenganal, Mallikarjun, Patil, Bharat, Reddy, B. S., Patil, D. H., Chakurte, Sidramappa, Kuchanur, P. H., Kumar K, Shiva, Gaddi, Ashok Kumar, Yogesh, L. N., Nidagundi, Jayaprakash, Dodamani, B. M., Sunkad, Gururaj, Thudi, Mahendar and Varshney, Rajeev K.. 2024. "Development and evaluation of Fusarium wilt-resistant and high-yielding chickpea advanced breeding line, KCD 11." The Plant Genome. 17 (2). https://doi.org/10.1002/tpg2.20460
Meta-QTL analysis reveals the important genomics regions for biotic stresses, nutritional quality and yield related traits in pearl millet
Gupta, Shreshth, Rangari, Sagar Krushnaji, Sahu, Aakash, Naik, Yogesh Dashrath, Satayavathi, C. Tara, Punnuri, Somashekhar and Thudi, Mahendar. 2024. "Meta-QTL analysis reveals the important genomics regions for biotic stresses, nutritional quality and yield related traits in pearl millet." CABI Agriculture and Bioscience. 5 (1). https://doi.org/10.1186/s43170-024-00230-5
Phenotypic profiling of lentil (Lens culinaris Medikus) accessions enabled identification of promising lines for use in breeding for high yield, early flowering and desirable traits
Naik, Yogesh Dashrath, Sharma, Vinay Kumar, Ask, Muraleedhar Sidaram, Rangari, Sagar Krushnaji, Kumar, Raj, Dikshit, Harsh Kumar, Sangita, Sahani, Kant, Ravi, Mishra, Gyan, Mir, Reyazul Rouf, Kudapa, Himabindu, Elango, Dinakaran, Zwart, Rebecca S., Varshney, Rajeev Kumar and Thudi, Mahendar. 2024. "Phenotypic profiling of lentil (Lens culinaris Medikus) accessions enabled identification of promising lines for use in breeding for high yield, early flowering and desirable traits ." Plant Genetic Resources: Characterization and Utilization. 22 (2), pp. 69-77. https://doi.org/10.1017/S1479262124000042
Meta-QTL analysis enabled identification of candidate genes and haplotypes for enhancing biotic stress resistance in chickpea
Isha, Ishita, Singh, Sarvjeet, Jha, Uday, Laxuman, C., Kudapa, Himabindu, Varshney, Rajeev K. V and Thudi, Mahendar. 2024. "Meta-QTL analysis enabled identification of candidate genes and haplotypes for enhancing biotic stress resistance in chickpea." Journal of Plant Biochemistry and Biotechnology. https://doi.org/10.1007/s13562-024-00873-5
Genomic approaches to enhance adaptive plasticity to cope with soil constraints amidst climate change in wheat
Bhoite, Roopali, Han, Yong, Alamuru, Alamuru Krishna, Varshney, Rajeev K. and Sharma, Darshan Lal. 2024. "Genomic approaches to enhance adaptive plasticity to cope with soil constraints amidst climate change in wheat." The Plant Genome. 17 (1). https://doi.org/10.1002/tpg2.20358
Major viral diseases in grain legumes: designing disease resistant legumes from plant breeding and OMICS integration
Jha, Uday Chand, Nayyar, Harsh, Chattopadhyay, Anirudha, Beena, Radha, Lone, Ajaz A., Naik, Yogesh Dashrath, Thudi, Mahendar, Prasad, Pagadala Venkata Vara, Gupta, Sanjeev, Dixit, Girish Prasad and Siddique, Kadambot H. M.. 2023. "Major viral diseases in grain legumes: designing disease resistant legumes from plant breeding and OMICS integration." Frontiers in Plant Science. 14. https://doi.org/10.3389/fpls.2023.1183505
Multi-locus genome-wide association study of chickpea reference set identifies genetic determinants of Pratylenchus thornei resistance
Channale, Sonal, Thompson, John P., Varshney, Rajeev K., Thudi, Mahendar and Zwart, Rebecca S.. 2023. "Multi-locus genome-wide association study of chickpea reference set identifies genetic determinants of Pratylenchus thornei resistance." Frontiers in Plant Science. 14. https://doi.org/10.3389/fpls.2023.1139574
Translational genomics for achieving higher genetic gains in groundnut
Pandey, Manish K., Pandey, Arun K., Kumar, Rakesh, Nwosu, Chogozie Victor, Guo, Baozhu, Wright, Graeme C., Bhat, Ramesh S., Chen, Xiaoping, Bera, Sandip K., Yuan, Mei, Jiang, Huifang, Faye, Issa, Radhakrishnan, Thankappan, Wang, Xingjun, Liang, Xuanquiang, Liao, Boshou, Zhang, Xinyou, Varshney, Rajeev K. and Zhuang, Weijian. 2020. "Translational genomics for achieving higher genetic gains in groundnut." Theoretical and Applied Genetics: international journal of plant breeding research. 133, pp. 1679-1702. https://doi.org/10.1007/s00122-020-03592-2
Genomic resources in plant breeding for sustainable agriculture
Thudi, Mahendar, Palakurthi, Ramesh, Schnable, James C., Chitikineni, Annapurna, Dreisigacker, Susanne, Mace, Emma, Srivastava, Rakesh K., Satyavathi, C. Tara, Odeny, Damaris, Tiwari, Vijay K., Lam, Hon-Ming, Hong, Yan Bin, Singh, Vikas K., Li, Guowei, Xu, Yunbi, Chen, Xiaoping, Kaila, Sanjay, Nguyen, Henry, Sivasankar, Sobhana, ..., Varshney, Rajeev K.. 2021. "Genomic resources in plant breeding for sustainable agriculture." Journal of Plant Physiology. 257, pp. 1-18. https://doi.org/10.1016/j.jplph.2020.153351
Major QTLs and Potential Candidate Genes for Heat Stress Tolerance Identified in Chickpea (Cicer arietinum L.)
Jha, Uday Chand, Nayyar, Harsh, Palakurthi, Ramesh, Jha, Rintu, Valluri, Vinod, Bajaj, Prasad, Chitikineni, Annapurna, Singh, Narendra P., Varshney, Rajeev K. and Thudi, Mahendar. 2021. "Major QTLs and Potential Candidate Genes for Heat Stress Tolerance Identified in Chickpea (Cicer arietinum L.)." Frontiers in Plant Science. 12, pp. 1-16. https://doi.org/10.3389/fpls.2021.655103
Legume Pangenome: Status and Scope for Crop Improvement
Jha, Uday Chand, Nayyar, Harsh, von Wettberg, Eric J. B., Naik, Yogesh Dashrath, Thudi, Mahendar and Siddique, Kadambot H. M.. 2022. "Legume Pangenome: Status and Scope for Crop Improvement." Plants. 11 (22). https://doi.org/10.3390/plants11223041
Integrated breeding approaches to enhance the nutritional quality of food legumes
Jha, Rintu, Yadav, Hemant Kumar, Raiya, Rahul, Singh, Rajesh Kumar, Jha, Uday Chand, Sathee, Lekshmy, Singh, Prashant, Thudi, Mahendar, Singh, Anshuman, Chaturvedi, Sushil Kumar and Tripathi, Shailesh. 2022. "Integrated breeding approaches to enhance the nutritional quality of food legumes." Frontiers in Plant Science. 13. https://doi.org/10.3389/fpls.2022.984700
Two decades of association mapping: Insights on disease resistance in major crops
Gangurde, Sunil S., Xavier, Alencar, Naik, Yogesh Dashrath, Jha, Uday Chand, Rangari, Sagar Krushnaji, Kumar, Raj, Reddy, M. S. Sai, Channale, Sonal, Elango, Dinakaran, Mir, Reyazul Rouf, Zwart, Rebecca, Laxuman, C., Sudini, Hari Kishan, Pandey, Manish K., Punnuri, Somashekhar, Mendu, Venugopal, Reddy, Umesh K., Guo, Baozhu, Gangarao, N. V. P. R., ..., Thudi, Mahendar. 2022. "Two decades of association mapping: Insights on disease resistance in major crops." Frontiers in Plant Science. 13. https://doi.org/10.3389/fpls.2022.1064059
Genome-wide association analysis to delineate high-quality SNPs for seed micronutrient density in chickpea (Cicer arietinum L.)
Fayaz, Humara, Tyagi, Sandhya, Wani, Aijaz A., Pandey, Renu, Akhtar, Sabina, Bhat, Mohd Ashraf, Chitikineni, Annapurna, Varshney, Rajeev Kumar, Thudi, Mahendar, Kumar, Upendra and Mir, Reyazul Rouf. 2022. "Genome-wide association analysis to delineate high-quality SNPs for seed micronutrient density in chickpea (Cicer arietinum L.)." Scientific Reports. 12 (1). https://doi.org/10.1038/s41598-022-14487-1
Genome-wide association mapping of seed oligosaccharides in chickpea
Elango, Dinakaran, Wang, Wanyan, Thudi, Mahender, Sebastiar, Sheelamary, Ramadoss, Bharathi Raja and Varshney, Rajeev K.. 2022. "Genome-wide association mapping of seed oligosaccharides in chickpea." Frontiers in Plant Science. 13. https://doi.org/10.3389/fpls.2022.1024543
Raffinose Family Oligosaccharides: Friend or Foe for Human and Plant Health?
Elango, Dinakaran, Rajendran, Karthika, der Laan, Liza Van, Sebastiar, Sheelamary, Raigne, Joscif, Thaiparambil, Naveen A., Hadda, Noureddine, Raja, Bharath, Wang, Wanyan, Ferela, Antonella, Chiteri, Kevin O., Thudi, Mahendar, Varshney, Rajeev K., Chopra, Surinder, Sing, Arti and Singh, Asheesh K.. 2022. "Raffinose Family Oligosaccharides: Friend or Foe for Human and Plant Health?" Frontiers in Plant Science. 13. https://doi.org/10.3389/fpls.2022.829118
Publisher Correction: Transcriptome analysis reveals key genes associated with root-lesion nematode Pratylenchus thornei resistance in chickpea
Channale Sonal, Kalavikatte, Danamma, Thompson J.P., Kudapa, Himabindu, Bajaj, Prasad, Varshney, Rajeev K., Zwart, Rebecca S. and Thudi, Mahendar. 2022. "Publisher Correction: Transcriptome analysis reveals key genes associated with root-lesion nematode Pratylenchus thornei resistance in chickpea ." Scientific Reports. 12 (1). https://doi.org/10.1038/s41598-022-08495-4
A Scintillating Journey of Genomics in Simplifying Complex Traits and Development of Abiotic Stress Resilient Chickpeas
Jaganathan, Deepa, Mallikarjuna, Bingi Pujari, Palakurthi, Ramesh, Samineni, Srinivasan, Laxuman, C., Bharadwaj, Chellapilla, Zwart, Rebecca, Fikre, Asnake, Gaur, Pooran, Varshney, Rajeev K. and Thudi, Mahendar. 2022. "A Scintillating Journey of Genomics in Simplifying Complex Traits and Development of Abiotic Stress Resilient Chickpeas." Kole, Chittaranjan (ed.) Genomic Designing for Abiotic Stress Resistant Pulse Crops. Cham, Switzerland. Springer. pp. 15-43
Transcriptome analysis reveals key genes associated with root‑lesion nematode Pratylenchus thornei resistance in chickpea
Channale, Sonal, Kalavikatte, Danamma, Thompson, John P., Kudapa, Himabindu, Bajaj, Prasad, Varshney, Rajeev K., Zwart, Rebecca S. and Thudi, Manhendar. 2021. "Transcriptome analysis reveals key genes associated with root‑lesion nematode Pratylenchus thornei resistance in chickpea." Scientific Reports. 11 (1), pp. 1-11. https://doi.org/10.1038/s41598-021-96906-3
Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits
Varshney, Rajeev K., Thudi, Mahendar, Roorkiwal, Manish, He, Weiming, Upadhyaya, Hari D., Yang, Wei, Bajaj, Prasad, Cubry, Philippe, Rathore, Abhishek, Jian, Jianbo, Doddamani, Dadakhalandar, Khan, Aamir W., Garg, Vanika, Chitikineni, Annapurna, Xu, Dawen, Gaur, Pooran M., Singh, Narendra P., Chaturvedi, Sushil K., Nadigatla, Gangarao V. P. R., ..., Liu, Xin. 2019. "Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits." Nature Genetics. 51, pp. 857-864. https://doi.org/10.1038/s41588-019-0401-3
Resistance to plant-parasitic nematodes in chickpea: current status and future perspectives
Zwart, Rebecca S., Thudi, Mahendar, Channale, Sonal, Manchikatla, Praveen K., Varshney, Rajeev K. and Thompson, John P.. 2019. "Resistance to plant-parasitic nematodes in chickpea: current status and future perspectives." Frontiers in Plant Science. 10, pp. 1-14. https://doi.org/10.3389/fpls.2019.00966
The first genetic map of pigeon pea based on diversity arrays technology (DArT) markers
Yang, Shi Ying, Saxena, Rachit K., Kulwal, Pawan L., Ash, Gavin J., Dubey, Anuja, Harper, John D. I., Upadhyaya, Hari D., Gothalwal, Ragini, Kilian, Andrzej and Varshney, Rajeev K.. 2011. "The first genetic map of pigeon pea based on diversity arrays technology (DArT) markers." Journal of Genetics. 90 (1), pp. 103-109. https://doi.org/10.1007/s12041-011-0050-5