Abstract
We constructed recombinant inbred lines (RILs) between a Japanese and a Taiwanese landrace of foxtail millet and employed next-generation sequencing, such as flexible ddRAD-seq and Nanopore sequencing to identify the candidate genes involved in the crop evolution of foxtail millet. We successfully constructed a linkage map using flexible ddRAD-seq with parents and RILs and detected major QTLs for each of three traits: leaf sheath colors, spikelet-tipped bristles (stb), and days to heading (DTH). (1) For leaf sheath colors, we identified the C gene on chromosome IV. (2) We identified a homeobox (HOX14) gene for stb on chromosome II, which shows homology with HvVrs1 in barley. (3) Finally, we identified a QTL with a large effect on DTH on chromosome II. A parent of the RILs from Taiwan and Yugu1 had a Harbinger-like TE in intron 3 of this gene. We also investigated the geographical distribution of the TE insertion type of this gene and found that the insertion type is distributed in the northern part of East Asia and intensively in South and Southeast Asia, suggesting that loss/reduction of function of this gene plays an important role in spreading into the northern part of East Asia and subtropical and tropical zones.
Highlights
We constructed recombinant inbred lines (RILs) between a Japanese and a Taiwanese landrace of foxtail millet and employed next-generation sequencing, such as flexible ddRAD-seq and Nanopore sequencing to identify the candidate genes involved in the crop evolution of foxtail millet
We investigated the geographical distribution of the transposable element (TE) insertion type of this gene and found that the insertion type is distributed in the northern part of East Asia and intensively in South and Southeast Asia, suggesting that loss/reduction of function of this gene plays an important role in spreading into the northern part of East Asia and subtropical and tropical zones
To confirm that the causative gene was HOX14, we performed an allelism test using a naturally occurring stb mutant of S. viridis (Supplementary Fig. S3), which we discovered in Japan, and designated "Kyoto stb-1." It seems that this S. viridis mutant occurred independently of JP73913
Summary
We constructed recombinant inbred lines (RILs) between a Japanese and a Taiwanese landrace of foxtail millet and employed next-generation sequencing, such as flexible ddRAD-seq and Nanopore sequencing to identify the candidate genes involved in the crop evolution of foxtail millet. Beauv.] is one of the oldest cereals in the Old World It is characterized by diploidy with small chromosome numbers (2n = 2x = 18), small genome size (approximately 500 Mb), an inbreeding habit, and a relatively short growth habit; it has become an ideal model plant for genetic studies on panicoid grass species, including switchgrass and Napier grass, which are considered as biofuel sources, and other cultivated millet species such as pearl m illet[1]. No population between distantly related landraces collected from different geographical conditions has been used for mapping
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