Transcriptome Analysis Reveals Unique Relationships Among<i>Eleusine</i>Species and Heritage of<i>Eleusine coracana</i>

Zhang, Hui; Hall, Nathan; Goertzen, Leslie R.; Chen, Charles Y.; Peatman, Eric; Patel, Jinesh; McElroy, J. Scott

doi:10.1534/g3.119.400214

Cited by 20 publications

(13 citation statements)

References 45 publications

(59 reference statements)

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“…However, the full origin of the finger millet allotetraploid genome is not well understood (Zhang et al, 2019). The allopolyploidization event from diploid A and B sub-genome progenitors to form the tetraploid crop ancestor (E. corocana subsp.…”

Section: Sub-genome-specific Diversification and Polyploidymentioning

confidence: 99%

“…Therefore, East Africa is considered the primary centre of diversity and India an important secondary centre. The immediate wild progenitor of finger millet is believed to have arisen in East Africa by hybridization between two diploid species, the first of which being E. indica, which still occurs widely across Africa and is considered the (maternal) donor of what has become finger millet's A sub-genome; and the second, still unknown (and now possibly extinct), diploid pre-B sub-genome donor (Liu et al, 2014;Zhang et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

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Genomic and phenotypic characterization of finger millet indicates a complex diversification history

Bančič

Odeny

et al. 2021

Preprint

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Advances in sequencing technologies mean that insights into crop diversification aiding future breeding can now be explored in crops beyond major staples. For the first time, we use a genome assembly of finger millet, an allotetraploid orphan crop, to analyze DArTseq single nucleotide polymorphisms (SNPs) at the sub-genome level. A set of 8,778 SNPs and 13 agronomic traits characterizing a broad panel of 423 landrace accessions from Africa and Asia suggested the crop has undergone complex, context-specific diversification consistent with a long domestication history. Both Principal Component Analysis and Discriminant Analysis of Principal Components of SNPs indicated four groups of accessions that coincided with the principal geographic areas of finger millet cultivation. East Africa, the considered origin of the crop, appeared the least genetically diverse. A Principal Component Analysis of phenotypic data also indicated clear geographic differentiation, but different relationships among geographic areas than genomic data. Neighbour-joining trees of sub-genomes A and B showed different features which further supported the crop’s complex evolutionary history. Our genome-wide association study indicated only a small number of significant marker-trait associations. We applied then clustering to marker effects from a ridge regression model for each trait which revealed two clusters of different trait complexity, with days to flowering and threshing percentage among simple traits, and finger length and grain yield among more complex traits. Our study provides comprehensive new knowledge on the distribution of genomic and phenotypic variation in finger millet, supporting future breeding intra- and inter-regionally across its major cultivation range.Core ideas8,778 SNPs and 13 agronomic traits characterized a panel of 423 finger millet landraces.4 clusters of accessions coincided with major geographic areas of finger millet cultivation.A comparison of phenotypic and genomic data indicated a complex diversification history.This was confirmed by the analysis of allotetraploid finger millet’s separate sub-genomes.Comprehensive new knowledge for intra- and inter-regional breeding is provided.

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Section: Sub-genome-specific Diversification and Polyploidymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genomic and phenotypic characterization of finger millet indicates a complex diversification history

Bančič

Odeny

et al. 2021

Preprint

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“…Previously, whole-genome transcriptome analysis was exercised in established inbred parental genotypes and their hybrids to study differential gene expression patterns in terms of gene action to correlate changes in yield gains in crops. Differential gene expression was recorded in maize [ 142 , 143 ], rice [ 144 ], wheat [ 145 ], sorghum [ 146 ], finger millet [ 147 ], chickpea [ 148 ], and pearl millet [ 149 ].…”

Section: Heterosis and Genomicsmentioning

confidence: 99%

Exploitation of Heterosis in Pearl Millet: A Review

Srivastava

Bollam

Pujarula

et al. 2020

Plants

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The phenomenon of heterosis has fascinated plant breeders ever since it was first described by Charles Darwin in 1876 in the vegetable kingdom and later elaborated by George H Shull and Edward M East in maize during 1908. Heterosis is the phenotypic and functional superiority manifested in the F1 crosses over the parents. Various classical complementation mechanisms gave way to the study of the underlying potential cellular and molecular mechanisms responsible for heterosis. In cereals, such as maize, heterosis has been exploited very well, with the development of many single-cross hybrids that revolutionized the yield and productivity enhancements. Pearl millet (Pennisetum glaucum (L.) R. Br.) is one of the important cereal crops with nutritious grains and lower water and energy footprints in addition to the capability of growing in some of the harshest and most marginal environments of the world. In this highly cross-pollinating crop, heterosis was exploited by the development of a commercially viable cytoplasmic male-sterility (CMS) system involving a three-lines breeding system (A-, B- and R-lines). The first set of male-sterile lines, i.e., Tift 23A and Tift18A, were developed in the early 1960s in Tifton, Georgia, USA. These provided a breakthrough in the development of hybrids worldwide, e.g., Tift 23A was extensively used by Punjab Agricultural University (PAU), Ludhiana, India, for the development of the first single-cross pearl millet hybrid, named Hybrid Bajra 1 (HB 1), in 1965. Over the past five decades, the pearl millet community has shown tremendous improvement in terms of cytoplasmic and nuclear diversification of the hybrid parental lines, which led to a progressive increase in the yield and adaptability of the hybrids that were developed, resulting in significant genetic gains. Lately, the whole genome sequencing of Tift 23D2B1 and re-sequencing of circa 1000 genomes by a consortium led by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) has been a significant milestone in the development of cutting-edge genetic and genomic resources in pearl millet. Recently, the application of genomics and molecular technologies has provided better insights into genetic architecture and patterns of heterotic gene pools. Development of whole-genome prediction models incorporating heterotic gene pool models, mapped traits and markers have the potential to take heterosis breeding to a new level in pearl millet. This review discusses advances and prospects in various fronts of heterosis for pearl millet.

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“…The tertiary gene pool comprises diploid species E. jaegeri (2 n = 2x = 20; DD genome), E. multiflora (2 n = 2x = 16; CC genome), and E. verticillata (2 n = 2x = 18). Additionally, it has been comprehensively established that the diploid E. indica (wild goosegrass) is the source of the A genome in FM, but wanting evidence still exists on the source of B genome (Devarumath et al 2005;Liu et al, 2014;Hatakeyama et al 2018;Zhang et al 2019). Nevertheless, research on those species could bring novel genes that can be introgressed into the cultivable FM to develop high-yielding and stress-tolerant varieties, particularly against extreme drought, heat, salinity, low nutrients, and the devastating FM blast disease, all exacerbated by climate change.…”

Section: Finger Millet Gene Pool and Distribution Of Genetic Diversity For Climate-smart Breedingmentioning

confidence: 99%

Genetic and genomic resources for finger millet improvement: opportunities for advancing climate-smart agriculture

Wambi

Tumwesigye²,

Otienno

et al. 2020

Journal of Crop Improvement

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Finger millet (FM; Eleusine coracana (L.) Gaertn.) is becoming increasingly vulnerable to various climate-induced stresses, because of which the genetic and genomic resources will be important for improving the crop in the 21 st century. Currently, sizable-untapped genetic resources exists that offer promise for FM improvement to biotic and abiotic stresses. Also, earlier reports elaborate on the potential FM genomic resources, such as molecular markers, genetic maps, and DNA sequence, but the data are scanty to support the efficient and accelerated delivery of the climate-smart FM varieties. This is partly attributable to the delayed availability of complete genome sequence (CGS) of FM. Following the latest developments in FM genomic research, based on the CGS, a diversity of genomic resources have been reported. The review, therefore, provided a detailed analysis on the FM genetic and genomic resourcesaided interventions that could contribute to the three pillars of Climate-smart agriculture (CSA) for addressing FM production challenges under changing climate. Exceptionally, it presented enriched information on additional useful sources of variation within FM genetic resources that have been screened for improving FM tolerance to various climate-induced stresses. Also, it presents the novel opportunities for CSA that could come as a result of the recent availability of CGS data for revolutionizing the development of cutting-edge-molecular breeding tools. Specifically, emphasis was placed on genome-wide-based technologies, such as genomic selection (GS), gene pyramiding, and gene expression with the second-generation genomic biotechnologies, such as TILLING and EcoTILLING that are wanting and have received little attention.

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Transcriptome Analysis Reveals Unique Relationships AmongEleusineSpecies and Heritage ofEleusine coracana

Cited by 20 publications

References 45 publications

Genomic and phenotypic characterization of finger millet indicates a complex diversification history

Genomic and phenotypic characterization of finger millet indicates a complex diversification history

Exploitation of Heterosis in Pearl Millet: A Review

Genetic and genomic resources for finger millet improvement: opportunities for advancing climate-smart agriculture

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