Genetic analyses of adaptive traits in pearl millet (Pennisetum glaucum (L.) R. Br.)

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Elucidation of the Genetic Diversity within Some In Situ Shea Germplasm in Ghana

Shea is an agroforestry tree species known primarily for its rich butter, which contains stearin and tocopherol, and has ultraviolet ray absorption property; it is used in cooking, body care and traditional medicines. This tree is, however, uncultivated and collection of its nuts by rural dwellers is threatened by increased urbanization with its accompanying land use pressure and the need for fuel wood for rural households. There is also increased demand for shea products worldwide necessitating the need for shea improvement strategies. At the apex of this improvement program lies the need for germplasm collection, characterization, conservation and utilization. In order to conserve elite shea materials amidst dwindling shea populations threatened by climate change, there is a need to develop shea germplasm banks based on the representation of genetic and phenotypic variation focusing on known traits. The objective of the study was to evaluate 282 shea accessions for germplasm conservation and to determine the genetic diversity of the collected materials to inform future collections and drive crop improvement strategies. Leaf traits were used to differentiate and group the selected materials. Leaf length ranged between 16.83 cm and 30.85 cm, and leaf blade length ranged between 12.28 cm and 20.68 cm. Petiole length varied between 5.53 cm and 10.2 cm and the blade to petiole ratio was from 1.41 to 2.69. Correlation studies revealed significant negative correlation between the latitude of collection and all leaf traits measured. There was significant positive correlation between blade length and petiole length (0.57), blade length and total leaf length (0.87) and petiole length and breadth (0.49). The collected materials were grouped at 90% into two, based on the morphological descriptors studied. Three different approaches were employed to genetically analyze the materials based on single nucleotide polymorphic markers (SNP). A phylogenetic tree was constructed based on the SNPs generated; this grouped the materials into three, with various subgroups. Principal coordinate analysis also produced three distinct groups with groupings not based on geographical area of collection. Discriminant analysis of principal components (DAPC) also confirmed three groupings. The genetic diversity of the collection was very low (Hs) = 0.0406, which is an indication of potential inbreeding within the shea populations. To conclude, there was higher variation within locations than between locations

Genomic Resources to Guide Improvement of the Shea Tree.

A defining component of agroforestry parklands across Sahelo-Sudanian Africa (SSA), the shea tree (Vitellaria paradoxa) is central to sustaining local livelihoods and the farming environments of rural communities. Despite its economic and cultural value, however, not to mention the ecological roles it plays as a dominant parkland species, shea remains semi-domesticated with virtually no history of systematic genetic improvement. In truth, shea's extended juvenile period makes traditional breeding approaches untenable; but the opportunity for genome-assisted breeding is immense, provided the foundational resources are available. Here we report the development and public release of such resources. Using the FALCON-Phase workflow, 162.6 Gb of long-read PacBio sequence data were assembled into a 658.7 Mbp, chromosome-scale reference genome annotated with 38,505 coding genes. Whole genome duplication (WGD) analysis based on this gene space revealed clear signatures of two ancient WGD events in shea's evolutionary past, one prior to the Astrid-Rosid divergence (116-126 Mya) and the other at the root of the order Ericales (65-90 Mya). In a first genome-wide look at the suite of fatty acid (FA) biosynthesis genes that likely govern stearin content, the primary determinant of shea butter quality, relatively high copy numbers of six key enzymes were found (KASI, KASIII, FATB, FAD2, FAD3, and FAX2), some likely originating in shea's more recent WGD event. To help translate these findings into practical tools for characterization, selection, and genome-wide association studies (GWAS), resequencing data from a shea diversity panel was used to develop a database of more than 3.5 million functionally annotated, physically anchored SNPs. Two smaller, more curated sets of suggested SNPs, one for GWAS (104,211 SNPs) and the other targeting FA biosynthesis genes (90 SNPs), are also presented. With these resources, the hope is to support national programs across the shea belt in the strategic, genome-enabled conservation and long-term improvement of the shea tree for SSA

Genomic resources to guide improvement of the shea tree

A defining component of agroforestry parklands across Sahelo-Sudanian Africa (SSA), the shea tree (Vitellaria paradoxa) is central to sustaining local livelihoods and the farming environments of rural communities. Despite its economic and cultural value, however, not to mention the ecological roles it plays as a dominant parkland species, shea remains semi-domesticated with virtually no history of systematic genetic improvement. In truth, shea’s extended juvenile period makes traditional breeding approaches untenable; but the opportunity for genome-assisted breeding is immense, provided the foundational resources are available. Here we report the development and public release of such resources. Using the FALCON-Phase workflow, 162.6 Gb of long-read PacBio sequence data were assembled into a 658.7 Mbp, chromosome-scale reference genome annotated with 38,505 coding genes. Whole genome duplication (WGD) analysis based on this gene space revealed clear signatures of two ancient WGD events in shea’s evolutionary past, one prior to the Astrid-Rosid divergence (116–126 Mya) and the other at the root of the order Ericales (65–90 Mya). In a first genome-wide look at the suite of fatty acid (FA) biosynthesis genes that likely govern stearin content, the primary determinant of shea butter quality, relatively high copy numbers of six key enzymes were found (KASI, KASIII, FATB, FAD2, FAD3, and FAX2), some likely originating in shea’s more recent WGD event. To help translate these findings into practical tools for characterization, selection, and genome-wide association studies (GWAS), resequencing data from a shea diversity panel was used to develop a database of more than 3.5 million functionally annotated, physically anchored SNPs. Two smaller, more curated sets of suggested SNPs, one for GWAS (104,211 SNPs) and the other targeting FA biosynthesis genes (90 SNPs), are also presented. With these resources, the hope is to support national programs across the shea belt in the strategic, genome-enabled conservation and long-term improvement of the shea tree for SSA

Genomic resources to guide improvement of the shea tree

A defining component of agroforestry parklands across Sahelo-Sudanian Africa (SSA), the shea tree (Vitellaria paradoxa) is central to sustaining local livelihoods and the farming environments of rural communities. Despite its economic and cultural value, however, not to mention the ecological roles it plays as a dominant parkland species, shea remains semi-domesticated with virtually no history of systematic genetic improvement. In truth, shea’s extended juvenile period makes traditional breeding approaches untenable; but the opportunity for genome-assisted breeding is immense, provided the foundational resources are available. Here we report the development and public release of such resources. Using the FALCON-Phase workflow, 162.6 Gb of longread PacBio sequence data were assembled into a 658.7 Mbp, chromosome-scale reference genome annotated with 38,505 coding genes. Whole genome duplication (WGD) analysis based on this gene space revealed clear signatures of two ancient WGD events in shea’s evolutionary past, one prior to the Astrid-Rosid divergence (116–126 Mya) and the other at the root of the order Ericales (65–90 Mya). In a first genome-wide look at the suite of fatty acid (FA) biosynthesis genes that likely govern stearin content, the primary determinant of shea butter quality, relatively high copy numbers of six key enzymes were found (KASI, KASIII, FATB, FAD2, FAD3, and FAX2), some likely originating in shea’s more recent WGD event. To help translate these findings into practical tools for characterization, selection, and genome-wide association studies (GWAS), resequencing data from a shea diversity panel was used to develop a database of more than 3.5 million functionally annotated, physically anchored SNPs. Two smaller, more curated sets of suggested SNPs, one for GWAS (104,211 SNPs) and the other targeting FA biosynthesis genes (90 SNPs), are also presented. With these resources, the hope is to support national programs across the shea belt in the strategic, genome-enabled conservation and long-term improvement of the shea tree for SSA.The Basic Research to Enhance Agricultural Development (BREAD) program (award #1543942), jointly funded by the National Science Foundation (NSF) and the Bill & Melinda Gates Foundation (BMGF); the CGIAR Research Program (CRP) on Forests, Trees, and Agroforestry (FTA) ; the CGIAR (ICRAF) Genebank Platform; European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Program; Ghent University; the AOCC and the UC Davis Seed Biotechnology Center.http://www.frontiersin.org/Plant_Scienceam2022BiochemistryGeneticsMicrobiology and Plant Patholog