qAC2, a novel QTL that interacts with Wx and controls the low amylose content in rice (Oryza sativa L.)

Abstract

This manuscript reports the fine mapping of a novel QTL, qAC2 controlling the low amylose in rice. The action mechanism of the qAC2 is also investigated by the analysis of genetic interactions to Wx (a), Wx (b), du1, du2 and du3. Amylose content of the rice (Oryza sativa L.) endosperm greatly affects starch properties and eating quality of cooked rice. Seeds of japonica rice cultivar Kuiku162 have low amylose content (AC) and good eating quality. Our analysis revealed a novel QTL, designated as qAC2 that contributed to the low AC of Kuiku162. qAC2 was fine mapped within a 74.9-kb region between two insertion and deletion markers, KID3001 and KID5101, on the long arm of chromosome 2. Seven genes are predicted in this region, but none of them is known to be related to the regulation of AC. The AC of a near-isogenic line (NIL110) carrying qAC2 (Kuiku), the Kuiku162 allele of qAC2, in the genetic background of japonica cultivar Itadaki was lower by 1.1% points than that of Itadaki. The chain length distributions of amylopectin were similar in NIL110 and Itadaki; therefore, the low AC of NIL110 was caused by a decrease in the actual AC, but not by a difference in the amylopectin structure. The interaction analyses revealed that qAC2 (Kuiku) has epistatic interaction with Wx (a). The qAC2 (Kuiku) has epistatic interactions with two loci, du1 and du2, on Wx (b), whereas the genetic effect of qAC2 (Kuiku) has additive to that of du3 on Wx (b). Thus, similar to du1 and du2, qAC2 may have a function related to Wx (b) mRNA splicing.

Mapping quantitative trait loci associated with starch paste viscosity in rice (Oryza sativa L.) under different environmental conditions

“…In this study, we identified 93 QTL in the whole population at multiple field locations with different environmental conditions, and we detected four stable pleiotropic regions on chromosomes 2, 6, 7 and 11, while we detected the unstable and minor QTL on other chromosomes. In agreement with previous studies (Aluko et al., ; Li et al., ; Sano et al., ; Takemoto‐Kuno et al., ; Zhang et al., ), these QTL were detected on chromosomes 2 and 6, these QTL cluster to the major qAC2 , Wx and ALK or qGC6 . At the same time, we also detected two novel major QTL clusters on chromosomes 7 and 11, temporarily named qRVA7 and qRVA11 .…”

“…Based on molecular marker linkage maps and genome sequencing data, many genes and QTL related to quality traits (mainly appearance and grain size) have been identified and exploited in rice (Xing & Zhang, ); these genes/QTL include GW2 , GS2 , GS3 , GS5 , GW5 , GW6 and GL7 (Fan et al., ; Hu et al., ; Song, Huang, Shi, Zhu, & Lin, ; Wang, Li et al., ; Wang, Xiong et al., ; Weng et al., ; Xu, Liu et al., ). In contrast, only a few rice genes and QTL related to milling, nutrition and cooking and eating quality have been cloned ( Wx , qAC2 , qGC6 , ALK , Chlalk5 and Du1 ) (He et al., ; Li et al., , ; Sano, Katsumata, & Okuno, ; Takemoto‐Kuno et al., ; Zeng et al., ).…”

Comparison of the chemical and textural properties of germ‐remaining soft rice grains from different spikelet positions

“…Previous studies have shown that in addition to the Wx gene, single-base mutations in other genes also can cause changes in AAC (Ando et al, 2010;Takemoto et al, 2015) . The reasons for changes in composition of endosperm starch are multifaceted, and the genetic basis of the material was the primary cause.…”

“…As a result, further studies are needed to discern whether this difference has a genetic basis. Previous studies have shown that in addition to the Wx gene, single-base mutations in other genes also can cause changes in AAC (Ando et al, 2010;Takemoto et al, 2015) . Second, the difference in starch composition was also related to different developmental conditions and the ambient temperature.…”

Marker-assisted selection in rice breeding programs in Hokkaido

“…Accurate understanding of the genetic structure and genes controlling virulence is required in management strategies for the durability of blast resistance in rice. Japanese market (Ando et al 2010, Sato et al 2002, Takemoto-Kuno et al 2015. The market in Japan evaluates rice products based on these traits.…”