Recombinant inbred lines and next-generation sequencing enable rapid identification of candidate genes involved in morphological and agronomic traits in foxtail millet

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.

Construction of a high-density genetic linkage map and QTL mapping for bioenergy-related traits in sweet sorghum [Sorghum bicolor (L.) Moench]

“…The obtained SNPs were distributed throughout the sorghum genome indicating the effectiveness of this technique, which made it possible to identify a large number of polymorphisms at a low cost ( Peterson et al., 2012 ). The ddRAD-Seq technique has recently been utilized successfully in a variety of plants, including foxtail millet ( Fukunaga et al., 2022 ), Brassica napus ( Chen et al., 2017 ; Scheben et al., 2020 ), and sesame ( Yol et al., 2021 ). To our knowledge, this study is the first to demonstrate that ddRAD-Seq is a suitable approach to detect variants at a genome-wide scale in the sorghum genome.…”

Molecular characterization and SNP identification using genotyping-by-sequencing in high-yielding mutants of proso millet

“…A total of 23,000 SNPs were identified from the study across the genomes ( Kumar et al., 2016 ). Next-generation sequencing of recombinant inbred lines (RILs) was performed to identify candidate genes controlling important morphological and agronomical traits in foxtail millet ( Fukunaga et al., 2022 ). In proso millet, the first linkage map and QTLs for agronomic traits were reported by Rajput et al.…”

Crop Evolution of Foxtail Millet

“…The other heading time-associated gene that was thoroughly examined is Pseudo-response regulator 37 ( SiPRR37 ). Recently, two research groups found that this gene plays an important role in the latitudinal adaptation of foxtail millet [ 99 , 100 ]. Li et al [ 99 ] investigated Chinese landraces of foxtail millet using a genome-wide association study (GWAS) and found that transposable element (TE) insertion into SiPRR37 was important for the adaptation of foxtail millet to Northeast China by genotyping 312 accessions (mostly from China), whereas Fukunaga et al [ 100 ] found TE insertion in a Taiwanese landrace by QTL analysis of recombinant inbred lines derived from a hybrid between a Japanese landrace and a Taiwanese landrace.…”

“…Recently, two research groups found that this gene plays an important role in the latitudinal adaptation of foxtail millet [ 99 , 100 ]. Li et al [ 99 ] investigated Chinese landraces of foxtail millet using a genome-wide association study (GWAS) and found that transposable element (TE) insertion into SiPRR37 was important for the adaptation of foxtail millet to Northeast China by genotyping 312 accessions (mostly from China), whereas Fukunaga et al [ 100 ] found TE insertion in a Taiwanese landrace by QTL analysis of recombinant inbred lines derived from a hybrid between a Japanese landrace and a Taiwanese landrace. They found that TE insertions are predominantly distributed in Southern Asia, such as the Nansei Islands of Japan, Taiwan, the Philippines, Indonesia, Thailand, Myanmar, Bangladesh, India, Nepal, Pakistan, and Afghanistan, as well as in Kenya, and they sporadically occur in Ukraine and East Asia, including China, Korea, and Japan, according to the genotyping of 99 foxtail millet landraces from Eurasia and Africa ( Figure 5 ).…”