Investigating Drought Tolerance in Chickpea Using Genome-Wide Association Mapping and Genomic Selection Based on Whole-Genome Resequencing Data

Li, Yongle; Ruperao, Pradeep; Batley, Jacqueline; Edwards, David; Khan, Tanveer; Colmer, Timothy D.; Pang, Jiayin; Siddique, Kadambot H. M.; Sutton, Tim

doi:10.3389/fpls.2018.00190

Cited by 110 publications

(93 citation statements)

References 94 publications

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“…Our data indicated that PI293469, PI349674, and PI293568 proved to successfully maintain this mechanism even at 21 d after drought stress. An attempt to unravel the mechanisms of drought tolerance in legumes such as chickpea (Cicer arietinum L.) was conducted by Li et al (2018). Candidate genes such as auxin efflux carrier protein (PIN3), p-glycoprotein, and nodulin MtN21/EamA-like transporter were identified to probably confer drought tolerance in chickpea.…”

Section: Discussionmentioning

confidence: 99%

Investigation on Various Aboveground Traits to Identify Drought Tolerance in Cowpea Seedlings

Ravelombola¹,

Shi²,

Qin³

et al. 2018

horts

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Impacts of drought stress on crop production can significantly impair farmer's revenue, hence adversely impacting the gross national product growth. For cowpea [Vigna unguiculata (L.) Walp.], which is a legume of economic importance, effects of drought at early vegetative growth could lead to substantial yield losses. However, little has been done with respect to breeding for cowpea cultivars withstanding drought at early vegetative growth. In addition, previous investigations have focused on how plant morphology and root architecture can confer drought tolerance in cowpea, which is not sufficient in efforts to unravel unknown drought tolerance-related genetic mechanisms, potentially of great importance in breeding, and not pertaining to either plant morphology or root architecture. Therefore, the objective of this study was to evaluate aboveground drought-related traits of cowpea genotypes at seedling stage. A total of 30 cowpea genotypes were greenhouse grown within boxes and the experimental design was completely randomized with three replicates. Drought stress was imposed for 28 days. Data on a total of 17 aboveground-related traits were collected. Results showed the following: 1) a large variation in these traits was found among the genotypes; 2) more trifoliate wilt/chlorosis tolerance but more unifoliate wilt/chlorosis susceptible were observed; 3) delayed senescence was related to the ability of maintaining a balanced chlorophyll content in both unifoliate and trifoliate leaves; and 4) the genotypes PI293469, PI349674, and PI293568 were found to be slow wilting and drought tolerant. These results could contribute to advancing breeding programs for drought tolerance in cowpea.

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Section: Discussionmentioning

confidence: 99%

Investigation on Various Aboveground Traits to Identify Drought Tolerance in Cowpea Seedlings

Ravelombola¹,

Shi²,

Qin³

et al. 2018

horts

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“…Until now, 236 plant genomes have been sequenced using next-generation sequencing technologies (Chen et al 2018) of varying quality. It can also be seen that some of the crops, which were considered as orphan crops in the last century, have now entered the next era of breeding and improvement after their genomes were sequenced and molecular breeding tools have been adopted for many of them, e.g., sorghum (Paterson et al 2009;Fernandes et al 2018), pearl millet (Varshney et al 2017;Liang et al 2018), peanut (Bertioli et al 2016;Varshney 2016;Janila et al 2016), chickpea (Varshney et al 2013, Li et al 2018, foxtail millet (Zhang et al 2012), tef (Cannarozzi et al 2014), finger millet (Hittalmani et al 2017), cowpea (Boukar et al 2018), bitter gourd (Urasaki et al 2017), and cucurbits (Zheng et al 2019). The AOCC-mandated genomes, if already sequenced and published, will be assessed for their quality and if needed will be corroborated using complementary sequencing technologies.…”

Section: Application Of Genomicsmentioning

confidence: 99%

African Orphan Crops Consortium (AOCC): status of developing genomic resources for African orphan crops

Hendre

Muthemba

Kariba

et al. 2019

Planta

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Main conclusion The African Orphan Crops Consortium (AOCC) successfully initiated the ambitious genome sequencing project of 101 African orphan crops/trees with 6 genomes sequenced, 6 near completion, and 20 currently in progress. Addressing stunting, malnutrition, and hidden hunger through nutritious, economic, and resilient agri-food system is one of the major agricultural challenges of this century. As sub-Saharan Africa harbors a large portion of the severely malnourished population, the African Orphan Crops Consortium (AOCC) was established in 2011 with an aim to reduce stunting and malnutrition by providing nutritional security through improving locally adapted nutritious, but neglected, under-researched or orphan African food crops. Foods from these indigenous or naturalized crops and trees are rich in minerals, vitamins, and antioxidant, and are an integral part of the dietary portfolio and cultural, social, and economic milieu of African farmers. Through stakeholder consultations supported by the African Union, 101 African orphan and under-researched crop species were prioritized to mainstream into African agri-food systems. The AOCC, through a network of international-regional-public-private partnerships and collaborations, is generating genomic resources of three types, i.e., reference genome sequence, transcriptome sequence, and re-sequencing 100 accessions/species, using next-generation sequencing (NGS) technology. Furthermore, the University of California Davis African Plant Breeding Academy under the AOCC banner is training 150 lead African scientists to breed high yielding, nutritious, and climate-resilient (biotic and abiotic stress tolerant) crop varieties that meet African farmer and consumer needs. To date, one or more forms of sequence data have been produced for 60 crops. Reference genome sequences for six species have already been published, 6 are almost near completion, and 19 are in progress.

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“…The mutation identified for the ABCB26 gene at q-3.3, which could contribute to the q-3.2 effect, is also interesting for further studies. This gene was in a recent study associated with grain yield in a GWAS study of chickpea accessions (Li et al 2018). Several of the ABCB transporters have a role in auxin transport, but the exact function for the ABCB26 transporters in plants has not been determined (Lefèvre and Boutry 2018).…”

Section: Qtl On Lg 3 (Q-32) Had a Central Role In The Regulation Of mentioning

confidence: 99%

Co-localization of genomic regions associated with seed morphology and composition in a desi chickpea (Cicer arietinum L.) population varying in seed protein concentration

et al. 2019

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Key message Major QTL on LG 1 and 3 control seed filling and seed coat development, thereby affecting seed shape, size, color, composition and weight, key determinants of crop yield and quality. Abstract A chickpea (Cicer arietinum L.) population consisting of 189 recombinant inbred lines (RILs) derived from a cross between medium-protein ICC 995 and high-protein ICC 5912 genotypes of the desi market class was analyzed for seed properties. Seed from the parental lines and RILs was produced in four different environments for determination of seed shape (SS), 100-seed weight (100-SW), protein (PRO) and starch (STA) concentration. Polymorphic genetic markers for the population were identified by Genotyping by Sequencing and assembled into a 522.5 cM genetic map. Phenotype data from the different growth environments were analyzed by QTL mapping done by single and multi-environment analyses and in addition, single marker association mapping. The analyses identified in total 11 QTL, of which the most significant (P < 0.05) loci were located on LG 1 (q-1.1), LG 2 (q-2.1), LG 3 (q-3.2, q-3.3), LG 4 (q-4.2), and LG 5 (q-5.1). STA was mostly affected by q-1.1, which explained 19.0% of the phenotypic variance for the trait. The largest QTL effects were demonstrated by q-3.2 that explained 52.5% of the phenotypic variances for 100-SW, 44.3% for PRO, and 14.6% for SS. This locus was also highly associated with flower color (COL; 95.2% explained) and showed q-3.2 alleles from the ICC 5912 parent conferred the blue flower color and production of small, round seeds with relatively high protein concentration. Genes affecting seed filling at q-1.1 and seed coat development at q-3.2, respectively, were considered to underlie differences in seed composition and morphology in the RIL population.Communicated by Henry T. Nguyen.Runfeng Wang and Manu P. Gangola have contributed equally to this work.Publisher's Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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Investigating Drought Tolerance in Chickpea Using Genome-Wide Association Mapping and Genomic Selection Based on Whole-Genome Resequencing Data

Cited by 110 publications

References 94 publications

Investigation on Various Aboveground Traits to Identify Drought Tolerance in Cowpea Seedlings

Investigation on Various Aboveground Traits to Identify Drought Tolerance in Cowpea Seedlings

African Orphan Crops Consortium (AOCC): status of developing genomic resources for African orphan crops

Co-localization of genomic regions associated with seed morphology and composition in a desi chickpea (Cicer arietinum L.) population varying in seed protein concentration

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