Polymorphism pattern at a miniature inverted‐repeat transposable element locus downstream of the domestication gene Teosinte‐branched1 in wild and domesticated pearl millet

Abstract

Unravelling the mechanisms involved in adaptation to understand plant morphological evolution is a challenging goal. For crop species, identification of molecular causal polymorphisms involved in domestication traits is central to this issue. Pearl millet, a domesticated grass mostly found in semi-arid areas of Africa and India, is an interesting model to address this topic: the domesticated form shares common derived phenotypes with some other cereals such as a decreased ability to develop basal and axillary branches in comparison with the wild phenotype. Two recent studies have shown that the orthologue of the maize gene Teosinte-Branched1 in pearl millet (PgTb1) was probably involved in branching evolution during domestication and that a miniature inverted-repeat transposable element (MITE) of the Tuareg family was inserted in the 3' untranslated region of PgTb1. For a set of 35 wild and domesticated populations, we compared the polymorphism patterns at this MITE and at microsatellite loci. The Tuareg insertion was nearly absent in the wild populations, whereas a strong longitudinal frequency cline was observed in the domesticated populations. The geographical pattern revealed by neutral microsatellite loci clearly demonstrated that isolation by distance does not account for the existence of this cline. However, comparison of population differentiation at the microsatellite and the MITE loci and analyses of the nucleotide polymorphism pattern in the downstream region of PgTb1 did not show evidence that the cline at the MITE locus has been shaped by selection, suggesting the implication of a neutral process. Alternative hypotheses are discussed.

Unexpected pattern of pearl millet genetic diversity among ethno-linguistic groups in the Lake Chad Basin

“…The mean intra-population H e was very similar to values found by Lakis et al (2012) in four villages of south-western Niger and by Dussert et al (2015) at a continental scale. Most populations displayed a mean heterozygosity deficit which has already been noticed by several authors (Lakis et al , 2012; Dussert et al , 2013). However, the mean deviation from Hardy–Weinberg expectations was very variable among populations, with a mean F IS varying from −0.21 to 0.24 (mean of 0.08).…”

From Many, One: Genetic Control of Prolificacy during Maize Domestication

“…Given the evidence that a Hopscotch transposon is the functional variant at tb1 [29], the transposons in the causative interval of gt1 are good candidates for future functional assays. Transposon inserts have also been identified in alleles of genes involved in millet and tomato domestication or improvement [44], [45], suggesting that transposons may be important contributors to regulator variation in crop plants.…”

Inference of domestication history and differentiation between early‐ and late‐flowering varieties in pearl millet

“…Twenty‐five of these populations had already been used in a previous study including mostly early‐flowering varieties (Dussert et al . ). The sampled populations were distributed from Senegal to Sudan, covering the whole distribution of domesticated and wild pearl millet in the Sahelian area.…”