Marker-Assisted Selection of Wheat Breeding in Japan

Varieties of wheat produced outside of Japan are much better suited to producing good quality bread, whereas domestic wheat is produced to be suitable for making Japanese noodles. In contrast, domestic varieties are superior in terms of agricultural performance (excluding yield, early maturity), Fusarium head blight resistance, and preharvest spouting resistance, as they are well adapted to Japanese climate conditions. Overseas varieties provide a useful genetic resource for improving the quality of domestic wheat for bread making. However, it is difficult to breed good quality wheat for bread making that also has high yield and resistance to both Fusarium head blight and preharvest sprouting from a single cross. Therefore, the backcross method is considered more reliable in improving domestic wheat quality for bread making.

'Setokirara' was released in 2013, having been bred using the backcross method and marker-assisted selection (Fig. 35.5). 'Fukuhonoka' was chosen as the recurrent parent. 'Fukuhonoka' is a soft wheat cultivar for Japanese noodles, and is well adapted to the temperate climate conditions in Japan. It has a high yield, good preharvest sprouting resistance, and acceptable Fusarium head blight resistance. To improve its bread quality, a triple homozygous genotype (Glu-D1d, Glu-B3h, and Pinb-D1c) was selected using a Polymerase Chain Reaction (PCR) marker. 'Setokirara' showed agricultural performance similar to that by 'Fukuhonoka' and quality of the same standard as that by HRW for bread making.

A combination of glutenin subunits Glu-D1a and Glu-B3g results in extra-strong flour (Maruyama-Funatsuki et al. 2004; Tabiki et al. 2006). 'Yumechikara' is an extra-strong Hard Red Winter wheat cultivar released in 2009 with a marker-assisted selection of these two subunits (Tabiki et al. 2011). Extra-strong flour has a unique bread-making quality. The bread-making quality score for 'Yumechikara' flour was superior to Canadian western No. 1 (1CW) when blended with domestic soft wheat flour (Fig. 35.6).

Fig. 35.5 Breeding of 'Setokirara' with good bread-making quality

Fig. 35.6 Bread-making quality of 'Yumechikara' blended with soft flour

Wheat yellow mosaic virus is a soil borne disease; outbreaks have been reported on the mainland since 1936, and in 1991, an outbreak was reported in Hokkaido, where half the quantity of domestic wheat is produced. There are many genetic varieties resistant to this disease; for example, 'Yumechikara' is highly resistant. In 2010, a gene, YmIb, located on the long arm of the 2D chromosome, was reported as conferring resistance to wheat yellow mosaic virus (Nishio et al. 2010). Markers for this gene were also reported, making it particularly useful, and a backcross program to breed resistant varieties is now in progress.

Preharvest sprouting (PHS) resistance is required for Japanese cultivars. In Japan, breeders use 'Zenkouzikomugi' as a genetic resource for PHS resistance. 'Zenkouzikomugi' has two quantitative trait loci (QTLs) for PHS resistance located on chromosomes 3A and 5A. One of these QTLs was assumed to be the Mother of FT and TFL1 (MFT) (Nakamura et al. 2011). Mapping analysis showed that MFT is colocated on chromosome 3A with the PHS-resistant QTL (Qphs.ocs-3A.1). Precocious germination of isolated immature embryos was suppressed by transient introduction of MFT driven by the maize ubiquitin promoter. This and further evidence showed that MFT is a germination repressor and may be the causal gene for Qphs.ocs-3A.1. A comparison of the genomic sequences of MFT-3A from Chinese spring (which is less PHS-resistant) and 'Zenkouzikomugi' (highly PHS-resistant) revealed single nucleotide polymorphism (SNP). A cleaved amplified polymorphic sequence (CAPS) marker was developed in this SNP.

The Zenkouzikomugi-type allele, which is highly PHS-resistant, is very popular in domestic wheat varieties. In contrast, the Zenkouzikomugi-type allele is very rare in foreign varieties, and the less resistant Chinese spring-type allele is more common. When only domestic varieties were used as cross parents to breed soft wheat for Japanese noodles, this MFT CAPS marker was useless because there was no polymorphism. However, when varieties from overseas were used to improve breadmaking quality, the MFT CAPS marker revealed its usefulness, and it has now started to be used alongside other markers (e.g., Glu-1, Glu-3, Gli-1, Pina-1, and Pinb-1). In the near future, a new variety will be released with the MFT CAPS marker.

There are three types of Fusarium head blight (FHB) resistance in wheat.

Type 1: Resistance to FHB initial infection

Type 2: Resistance to FHB spread within the spike derived from the initial infection Type 3: Decomposition or lack of accumulation of mycotoxins of FHB

In 2011, 'Wheat Norin PL-9' was bred from a cross between 'U24' (cleistogamous [closed flowering]) and 'Saikai 165' (chasmogamous [open flowering]) (Kubo et al. 2012). 'U24' is a cleistogamous line with type 1 FHB resistance (Kubo et al. 2010, 2013). However, its agricultural performance is poor (late maturity, long culm length). 'Saikai 165' is a derivative of 'Sumai 3', which is globally the most popular FHB-resistant genetic resource. 'Saikai 165' and 'Sumai 3' have a QTL (Fhb1) for type 2 FHB-resistance located on the short arms of chromosome 3B. 'Wheat Norin PL-9' has a cleistogamous characteristic that increases its resistance to initial infection by FHB; it also incorporates a Saikai 165 (resistant) genotype in Fhb1, which was selected by a PCR-marker. It showed similar levels of resistance to the spread of FHB and mycotoxin accumulation as 'Saikai 165', and a better agricultural performance than 'U24'. However, we still need to see an improvement in agricultural performance before releasing a new variety with both type 1and type 2-resistance to FHB.

Table 35.1 shows the molecular markers used in wheat breeding in Japan. Molecular markers for flour color and yield will be developed in the next few years. Grain yield is an important character for increasing domestic wheat production. However, much further research is needed in order to elucidate the mechanisms driving high yield under Japanese climate conditions before a molecular marker can be developed.

Table 35.1 Use of molecular markers in wheat breeding in Japan



Status of application

Amylose content (stickiness, shelf life)


In current application

Dough strength

Glu-1, Glu-3, Gli-1

In current application

Grain hardness (damaged starch)

Pina-1, Pinb-1

In current application

Wheat yellow mosaic virus


In current application

Preharvest sprouting

MFT (Mother of FT and TFL1)

In current application

Fusarium head blight


In current application


Vrn, Ppd

In validation

Flour color


Basic research/development

Flour yield


Basic research/development

Grain yield


Not yet

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