Development of gene-tagged markers for quantitative trait loci underlying rice yield components

Abstract

Higher yields of rice have always been a predominant goal in rice breeding techniques. However, the inheritances of rice yield and its components are still unknown, and no information regarding suitable alleles can be directly provided for improving the rice yield level until three major quantitative trait loci (QTLs) have been cloned and functionally characterized. These QTLs contain Gn1a for grain number per panicle and GS3 and GW2 for grain weight. It has been proven that these three genes show a potential in improving the rice yield level. However, the distribution of suitable alleles on these three loci in rice cultivars and germ plasm are yet to be elucidated, this retards the progress of the utilization of suitable alleles in rice breeding techniques to produce higher yields. In the present study, we developed a set of gene-tagged markers based on the gene mutation sites Gn1a-M1 and Gn1a-M2 for Gn1a, GW2-HapI for GW2, and GS3-PstI for GS3. The results demonstrated that these STS markers could clearly differentiate between the different alleles at each gene locus. A survey of the allele distributions of the abovementioned three genes was performed with 156 cultivars. It was observed that the 5150-Gn1a allele was absent on the Gn1a locus and only two type alleles (Ha-Gn1a and Ko-Gn1a) were present, of which 54.3% indica and 21.5% japonica cultivars contained the Ha-Gn1a allele. Two alleles (MH-GS3 and ZS-GS3) were detected on the GS3 locus, and 48.6% indica and 9.9% japonica cultivars harbored the suitable allele MH-GS3. Further, all the cultivars contained the FA-GW2 allele on GW2, whereas the WY-GW2 allele was not found. These results further suggested that some of the alleles residing in the indica subspecies have introgressed into the japonica group with a very low frequency. The gene-tagged markers developed in the present study can be directly used as a tool for marker-aided selection (MAS) in rice breeding techniques to produce higher yields.

Comparative Mapping Suggests Repeated Selection of the Same Quantitative Trait Locus for High Leaf Photosynthesis Rate in Rice High‐Yield Breeding Programs

“…Because real‐time measurements of photosynthesis are laborious and easily influenced by environmental changes, they are not generally appropriate for genetic analysis. We have established some rapid and precise methods to indirectly evaluate photosynthesis by measuring related traits (Takai et al, 2006a, 2009, 2010a, 2010b). For example, the SPAD value and LNC, which reflect chlorophyll content and the amount of the ribulose‐1,5‐bisphosphate carboxylase oxygenase (Rubisco) protein, can be easily measured using a SPAD meter and a N and C analyzer, respectively.…”

“…Koshihikari is a leading japonica variety in Japan (Yamamoto et al, 2010), but its yields are relatively low compared to indica and indica – japonica varieties or something similar. Takanari is one of the highest yielding japonica – indica varieties in Japan (Imbe et al, 2004) with a greater photosynthetic rate in the flag leaves at the heading stage than Koshihikari (Ohsumi et al, 2007; Takai et al, 2010b). Tongil is a high‐yielding indica variety grown in Korea (Chung and Heu, 1980).…”

Features of the photosynthetic tissue in the sheaths of rice (Oryza sativaL.)

“…Because of this, the studies on rice photosynthesis are only focused on rice blade up to now [12]. However, in this study, we found that rice sheath was also rich in photosynthetic cells in its outer epidermis ( Fig.…”

“…To solve this problem, attention has been paid in recent years to the photosynthesis of high-yielding rice varieties [2][3]. The different aspects of the photosynthesis in high-yielding rice varieties have been studied by many researchers, such as high photosynthetic efficiency [4][5], efficiency of solar energy utilization [6], distribution of assimilates [7], leaf senescence [8], environmental stresses [9], ideal plant type of super hybrid rice [10][11], stomata [7], genetic expression [12], and so on. Heterosis of rice was used in China and new high photosynthetic rice varieties such as super hybrid rice were cultured, which showed the morphological features including its long, narrow, and erect top leaves [10,13], which is characterized as ideal plant type rice [13] and this type of rice is reported to trap more solar energy [3,10].…”

Identification of QTLs for agronomic traits in indica rice using an RIL population

“…GS3 is a major QTL for grain length and grain weight and a minor QTL for grain width (Fan et al 2006). Yan et al (2009) and Xu et al (2015b) have developed markers for the functional site or tightly linked sites of GS3. qGL3 is a major QTL for grain length, encoding a putative protein phosphatase with Kelch-like repeat domain (OsPPKL1) (Zhang et al 2012).…”