Waxy allele diversification in foxtail millet (Setaria italica) landraces of Taiwan

Abstract

Foxtail millet (Setaria italica (L.) P. Beauv.), the second most cultivated millet species, is well adapted to diverse environments and remains an important cereal food and forage crop in arid and semiarid regions worldwide. A symbolic crop for indigenous Austronesian peoples, foxtail millet has been cultivated in Taiwan for more than 5,000 years, and landraces reflect diversifying selection for various food applications. A total of 124 accessions collected within Taiwan were assessed for Wx genotypes. Four identified Wx alleles, I, III, IV, and IX were caused by insertion of various transposable elements (TEs) and resulted in endosperm with non-waxy, low amylose content (AC), and waxy, respectively. A total of 16.9%, 4.0%, 49.2%, and 29.8% of accessions were classified as type I, III, IV, and IX, respectively; approximately half of the accessions belonged to the waxy type, indicating that glutinous grains were favored for making traditional food and wine. The TE insertion affected splicing efficiency rather than accuracy, leading to significantly reduced expression of wx in types III, IV, and IX, although their transcripts were the same as wild-type, type I. Consequently, the granule-bound starch synthase I (GBSSI) contents of the three mutated genotypes were relatively low, leading to waxy or low AC endosperm, and the Wx genotypes could explain 78% of variance in AC. The geographic distribution of Wx genotypes are associated with culinary preferences and migration routes of Taiwanese indigenous peoples—in particular, the genotype of landraces collected from Orchid Island was distinct from those from Taiwan Island. This information on the major gene regulating starch biosynthesis in foxtail millet endosperm can be applied to breeding programs for grain quality, and contributes to knowledge of Austronesian cultures.

Genetic Variation of Physicochemical Properties and Digestibility of Foxtail Millet (Setaria italica) Landraces of Taiwan

“…The estimated AC of these 92 accessions of foxtail millet ranged from 0.7% to 16.9% (Table 1). According to a Wx genotyping assay, the AC of non-waxy genotypes ranged from 5.42% to 16.92%, which would be classified as low-AC types according to a previous study [9,10,30]. Consequently, in our study, the Q1 value of the AC of the non-waxy genotype was used to differentiate non-waxy and low-AC phenotypes.…”

“…Non-waxy wild-type foxtail millets are distributed over Eurasia, East Asia, and South Asia; nevertheless, more than half of landraces collected from Taiwan are the waxy type because of indigenous peoples’ preferences. The low AC accessions of Nakayama’s collection could be found in Taiwan and Southeast Asia only; additionally, the non-waxy landraces from Taiwan and Southeast Asia showed slightly lower AC than those from South Asia and countries to the west [9,10]. The non-waxy type of foxtail millet is generally used as forage or for being directly cooked and consumed like rice, while the waxy type is often fermented for alcoholic beverages, or eaten in the form of sticky cake and foxtail millet dumplings [10].…”

“…Foxtail millet grain was classified into three types based on AC, i.e., non-waxy, low-AC, and waxy. The non-waxy type was distributed worldwide, while the waxy type was distributed only in East Asia and Southeast Asia, accounting for almost half of the foxtail millet collection in Taiwan [9,10]. Starch viscosity is one of the key sensory parameters for cereal food processing, and can be assessed by the rapid viscosity analyzer (RVA), a useful tool for determining physicochemical properties to evaluate eating and cooking quality of cereal grains [11,12].…”

“…Understanding starch properties would greatly support the improvement of sensory and textural properties of foxtail millet for uses in daily staple diet items and food industries. In Taiwan, 50.1% of landraces belong to the waxy type, and the investigation of traditional uses of foxtail millet from five ethnic groups revealed that waxy foxtail millets were for brewing and making dumplings, whereas non-waxy or low-AC grains were for porridge [10].…”

Genetic Diversity of Landraces and Improved Varieties of Rice (Oryza sativa L.) in Taiwan

“…In Taiwan, 16 o cially acknowledged indigenous peoples have their own cultures and diet preferences, including diversi ed crop germplasm. Waxy genotypes of Taiwanese foxtail millet landraces were associated with various culinary and cultural preferences, leading to genetic variation of physicochemical properties and digestibility (Kuo et al 2018;Yin et al 2019).…”