Dataset Information

Transcriptomic analysis, genic SSR development, and genetic diversity of proso millet (Panicum miliaceum; Poaceae).

ABSTRACT: PREMISE OF THE STUDY:Proso millet (Panicum miliaceum; Poaceae) is a minor crop with good nutritional qualities and strong tolerance to drought stress and soil infertility. However, studies on genetic diversity have been limited due to a lack of efficient genetic markers. METHODS:Illumina sequencing technology was used to generate short read sequences of proso millet, and de novo transcriptome assemblies were used to develop a de novo assembly of proso millet. Genic simple sequence repeat (SSR) markers were identified and used to detect polymorphism among 56 accessions. Population structure and genetic similarity coefficient were estimated. RESULTS:In total, 25,341 unique gene sequences and 4724 SSR loci were obtained from the transcriptome, of which 229 pairs of SSR primers were validated, which resulted in 14 polymorphic genic SSR primers exhibiting 43 total alleles. According to the ratio of polymorphic markers (6.1%, 14/229), there are potentially 288 polymorphic genic SSR markers available for genetic assay development in the future. Bayesian population analyses showed that the 56 accessions comprised two distinct groups. DISCUSSION:A genetic structure and cluster assay indicated that the accessions from the Loess Plateau of China shared a high genetic similarity coefficient with those from other regions and that there was no correlation between genetic diversity and geographic origin. The transcriptome sequencing data and millet-specific SSR markers developed in this study establish an excellent resource for gene discovery and may improve the development of breeding programs in proso millet in the future.

SUBMITTER: Hou S

PROVIDER: S-EPMC5546162 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature

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Transcriptomic analysis, genic SSR development, and genetic diversity of proso millet (<i>Panicum miliaceum</i>; Poaceae).

Hou Siyu S Sun Zhaoxia Z Li Yaoshen Y Wang Yijie Y Ling Hubin H Xing Guofang G Han Yuanhuai Y Li Hongying H

Applications in plant sciences 20170728 7

<h4>Premise of the study</h4>Proso millet (<i>Panicum miliaceum</i>; Poaceae) is a minor crop with good nutritional qualities and strong tolerance to drought stress and soil infertility. However, studies on genetic diversity have been limited due to a lack of efficient genetic markers.<h4>Methods</h4>Illumina sequencing technology was used to generate short read sequences of proso millet, and de novo transcriptome assemblies were used to develop a de novo assembly of proso millet. Genic simple s ...[more]

PMID: 28791202

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Project description:Current agricultural production depends on very limited species grown as monocultures that are highly vulnerable to climate change, presenting a threat to the sustainability of agri-food systems. However, many hundreds of neglected crop species have the potential to cater to the challenges of climate change by means of resilience to adverse climate conditions. Proso millet (Panicum miliaceum L.), one of the underutilised minor millets grown as a rainfed subsistence crop, was selected in this study as an exemplary climate-resilient crop. Using a previously calibrated version of the Agricultural Production Systems Simulator (APSIM), the sensitivity of the crop to changes in temperature and precipitation was studied using the protocol of the Coordinated Climate Crop Modelling Project (C3MP). The future (2040-2069) production was simulated using bias-corrected climate data from 20 general circulation models of the Coupled Model Intercomparison Project (CMIP5) under RCP4.5 and 8.5 scenarios. According to the C3MP analysis, we found a 1°C increment of temperature decreased the yield by 5-10% at zero rainfall change. However, Proso millet yields increased by 5% within a restricted climate change space of up to 2°C of warming with increased rainfall. Simulated future climate yields were lower than the simulated yields under the baseline climate of the 1980-2009 period (mean 1707 kg ha-1) under both RCP4.5 (-7.3%) and RCP8.5 (-16.6%) though these changes were not significantly (p > 0.05) different from the baseline yields. Proso millet is currently cultivated in limited areas of Sri Lanka, but our yield mapping shows the potential for expansion of the crop to new areas under both current and future climates. The results of the study, indicating minor impacts from projected climate change, reveal that Proso millet is an excellent candidate for low-input farming systems under changing climate. More generally, through this study, a framework that can be used to assess the climate sensitivity of underutilized crops was also developed.

Dataset Information

Transcriptomic analysis, genic SSR development, and genetic diversity of proso millet (Panicum miliaceum; Poaceae).

Publications

Transcriptomic analysis, genic SSR development, and genetic diversity of proso millet (<i>Panicum miliaceum</i>; Poaceae).

Similar Datasets

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