The qSAC3 locus from indica rice effectively increases amylose content under a variety of conditions

Abstract

Background: Amylose content (AC) is a critical factor for the quality of rice. It is determined by the biosynthesis gene Waxy (Wx) and a variety of quantitative trait loci (QTLs). Although many QTLs have been reported to affect rice AC, few of them have been investigated under varying growth conditions, especially various temperatures, which are known to greatly influence the AC.

Results: We analyzed the AC at different temperatures and planting seasons in a set of chromosome segment substitution lines (CSSLs) which were derived from a cross between the indica variety 9311 and the japonica variety Nipponbare carrying the same Wx^b allele. A joint analysis detected a single locus, qSAC3, with a high logarithm of odds (LOD) score in four different conditions. The qSAC3 from indica 9311 (qSAC3^ind) substantially increased the AC in japonica Nipponbare under all tested growth conditions. Furthermore, introducing the qSAC3^ind into the soft rice variety Nangeng9108 with Wx^mq, a mutant allele of Wx^b, also moderately increased its AC and improved its appearance quality significantly by reducing the chalkiness of the polished rice.

Conclusions: Our results indicate that the qSAC3^ind could increase the AC of japonica rice in different environments as well as in the background of different Wx alleles and that qSAC3 is a valuable locus for fine-tuning the rice AC and ameliorating the dull endosperm in rice varieties with the Wx^mq allele.

Keywords: Amylose content; Chromosome segment substitution lines; Environmental effect; Quantitative trait loci; Rice quality.

Fig. 1

Amylose content of background parent Nipponbare and chromosome segment substitution lines under different conditions. Rice grains were filling at HT (high temperature, a), RT (room temperature, b), NS (normal season, c) and LS (late season, d) conditions. AC, Amylose content; NIP, Nipponbare

Fig. 2

QTL analysis of rice AC at different environmental conditions. The gray line indicates the threshold of the LOD score, 2.97 (p = 0.05). The arrow indicates the location of qSAC3, which has an LOD score of 3.144

Fig. 3

Genotype and phenotype of HZ1218. a Resequencing result of HZ1218. The red area indicates the substituted segment from 9311, and the blue area indicates background parent genotype. The short substituted segment on chromosome 3 in HZ1218 is the location of qSAC3. Molecular markers Y6665, Y7237, Y8113 and Y8212 are near the locus qSAC3. b PCR detection of HZ1218 by molecular markers Y6665, Y7237, Y8113 and Y8212. The results showed that the substituted segment on chromosome 3 contains Y7237 and Y8113 but not Y6665 and Y8212. c Rice AC of HZ1218 and NIP under different conditions. d Difference of rice AC (D-value = (AC_CSSL-AC_NIP)/AC_NIP) between HZ1218 and NIP in different conditions. Significant differences were determined by Student’s t-test, p-value < 0.01(**)

Fig. 4

Introduction of qSAC3^ind into Nangeng9108 improves rice quality. (a) Generation of NILs-qSAC3 (JS02–08 and JS34) by crossing Nangeng9108 with the CSSL HZ1213. b AC of Nangeng9108 (NG9108) and NILs-qSAC3 (JS02, 03, 04 and 34). c Polished rice of Nangeng9108 and JS04. d Chalkiness of Nangeng9108 (NG9108) and NILs-qSAC3 (JS02, 03, 04 and 34). Significant differences were determined by Student’s t-test, p-value < 0.01(**)