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doi:10.1038/nindia.2017.120 Published online 18 September 2017

Gene sequencing promises better days for millets

K. S. Jayaraman

The sequencing project gives new genetic insights into pearl millet's traits.
© ICRISAT
An international team of agriculture scientists has reported the whole genome sequencing of pearl millet (Cenchrus americanus (L.) Morrone) unleashing genomic data that will help improve crops of this staple food for more than 90 million people living in arid and semi-arid zones of Africa and Asia1

Despite its importance as food and as a source of straw for fodder and fuel, productivity of pearl millet (called 'babala' in Africa and 'bajra' in Hindi) has remained low — just 900 kg/hectare. It is also vulnerable to several diseases including downy mildew. 

Information gained from the sequencing study carried out at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) in Hyderabad, India, along with BGI-Shenzhen, China and the French National Research Institute for Sustainable Development (IRD), promises to change all this. One of the key outcomes of the sequencing study is the analysis of genetic variability to better understand the ability of this dryland cereal to survive soaring temperatures (over 42ºC) and its exceptional drought tolerance. 

Genome sequence can provide information about specific genomic regions or specific genes associated with agronomically important traits, including grain and fodder yield. The research team sequenced the whole genome of a reference genotype of pearl millet — which contains an estimated 38,579 protein-coding genes — and identified those which contribute to heat and drought tolerance. 

Besides, they "resequenced" genomic regions of interest — a key step in detection of mutations — and analysed almost 1,000 pearl millet lines, to establish "markers" for selection of promising parental lines for out-crossing. "We show the use of the genome sequence and resequencing information to make predictions of hybrid performance," their report says. "After inspecting predicted hybrid performance of single-cross combinations, we identified 159 pairs of (parental) lines that have so far not been used for hybrid breeding but can exhibit high hybrid performance." 

The researchers say their analysis of resequencing data together with phenotyping data for 20 traits for genomic selection "suggests that simultaneous improvement of grain and stover (fodder) yield might be feasible in pearl millet." Grain and fodder yield performance of hybrids in India have indeed improved over the past 50 years, "but our analysis shows there is potential for further improvements," the authors say.

The draft genome and resequencing data will help researchers better understand the trait variation while advancing genetic improvement of the crop. "For instance, we identified 1,054 markers for 15 agronomic traits that will be useful for pearl millet breeding." 

The researchers say the identification of gene families associated with the exceptional drought and heat tolerance "might enable engineering of not only pearl millet but also other cereal crops like rice, maize and wheat, which are currently able to provide only limited produce in arid or semi-arid regions."


References

1. Varshney, R. K. et al. Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. Nat. Biotechnol. (2017) doi: 10.1038/nbt.3943