QTL mapping reveals a tight linkage between QTLs for grain weight and panicle spikelet number in rice

Rice, Dec 2013

Background A number of QTL studies reported that one genomic region was associated with several traits, indicating linkage and/or pleiotropic effects. The question of pleiotropy versus tight linkage in these studies should be solved using a large-size population combined with high-density mapping. For example, if each of the 2 parents has a TGW-increasing or SPP-increasing QTL that is tightly linked, complementary combination of the 2 beneficial QTLs by using molecular markers could produce higher yields compared to the 2 parents. However, a pleiotropic QTL with opposite effects on the SPP and 1,000-grain weight (TGW) is complicated and challenging in terms of its application to rice improvement. Results In this study, using a series of BC5F4 nearly isogenic lines (NILs) that were derived from a cross between the Korean japonica cultivar Hwayeongbyeo and Oryza rufipogon, we demonstrated that 2 QTLs, qSPP5 for spikelets per panicle (SPP) and qTGW5 for grain weight (TGW), are tightly linked on chromosome 5. Alleles from the O. rufipogon parent increased the SPP and decreased TGW in the Hwayeongbyeo background. qSPP5 was located within a 803-kb interval between the simple sequence repeat (SSR) markers INDEL3 and RM18076. Based on the map position, qTGW 5 seemed to be the same gene as qSW5, which controls grain morphology. The additive effect of the O. rufipogon allele at qSPP5 was 10–15 SPP, and 33.0% of the phenotypic variance could be explained by the segregation of the SSR marker RM18058. Yield trials with BC5F4 NILs showed that lines that contained a homozygous O. rufipogon introgression at the qSPP5 region out-yielded sibling NILs that contained Hwayeongbyeo DNA by 15.3% and out-yielded the Hwayeongbyeo parent by 7.3%. Conclusion Based on the finding that the O. rufipogon allele for the SPP was beneficial in the japonica and indica cultivar backgrounds, the qSPP5 allele could be valuable for improving rice yields. In addition, the NIL populations and molecular markers are useful for cloning qSPP5.

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QTL mapping reveals a tight linkage between QTLs for grain weight and panicle spikelet number in rice

Xiao Luo 0 Shi-Dong Ji 2 Ping-Rong Yuan 1 Hyun-Sook Lee 0 Dong-Min Kim 0 Sangshetty Balkunde 0 Ju-Won Kang 0 Sang-Nag Ahn 0 0 Department of Agronomy, College of Agriculture & Life Sciences, Chungnam National University , Daejeon 305-764, Korea 1 Institute of Food Crop Research, Yunnan Academy of Agricultural Sciences , Kunming 650205, Yunnan, China 2 Nanyang Normal University , Nanyang City 473061, Henan Province, China Background: A number of QTL studies reported that one genomic region was associated with several traits, indicating linkage and/or pleiotropic effects. The question of pleiotropy versus tight linkage in these studies should be solved using a large-size population combined with high-density mapping. For example, if each of the 2 parents has a TGW-increasing or SPP-increasing QTL that is tightly linked, complementary combination of the 2 beneficial QTLs by using molecular markers could produce higher yields compared to the 2 parents. However, a pleiotropic QTL with opposite effects on the SPP and 1,000-grain weight (TGW) is complicated and challenging in terms of its application to rice improvement. Results: In this study, using a series of BC5F4 nearly isogenic lines (NILs) that were derived from a cross between the Korean japonica cultivar Hwayeongbyeo and Oryza rufipogon, we demonstrated that 2 QTLs, qSPP5 for spikelets per panicle (SPP) and qTGW5 for grain weight (TGW), are tightly linked on chromosome 5. Alleles from the O. rufipogon parent increased the SPP and decreased TGW in the Hwayeongbyeo background. qSPP5 was located within a 803-kb interval between the simple sequence repeat (SSR) markers INDEL3 and RM18076. Based on the map position, qTGW5 seemed to be the same gene as qSW5, which controls grain morphology. The additive effect of the O. rufipogon allele at qSPP5 was 10-15 SPP, and 33.0% of the phenotypic variance could be explained by the segregation of the SSR marker RM18058. Yield trials with BC5F4 NILs showed that lines that contained a homozygous O. rufipogon introgression at the qSPP5 region out-yielded sibling NILs that contained Hwayeongbyeo DNA by 15.3% and out-yielded the Hwayeongbyeo parent by 7.3%. Conclusion: Based on the finding that the O. rufipogon allele for the SPP was beneficial in the japonica and indica cultivar backgrounds, the qSPP5 allele could be valuable for improving rice yields. In addition, the NIL populations and molecular markers are useful for cloning qSPP5. - Background Asian cultivated rice (Oryza sativa L.) originated from common wild rice (Oryza rufipogon Griff.), and their morphological, biochemical and genetic relationships have been analyzed in many studies (Sun et al., 2001; Cai & Morishima 2002). Much of its genetic architecture and phenotypic construction changed during domestication from wild rice. In general, Oryza sativa is different from O. rufipogon in terms of a number of traits such as plant height, number of spikelets per panicle (SPP), 1000-grain weight, grain shape, and awn. Among these agronomic traits, the SPP and 1000-grain weight are determinants of grain yield (YD). The number of primary and secondary branches (SBs) strongly influences the average number of SPP (Yamagishi et al., 2002). QTLs for the SPP have been detected using various segregating populations (Kobayashi et al., 2004). Several QTLs for the SPP have also been identified in wild relatives (Thomson et al., 2003; Suh et al., 2005; Onishi et al., 2007). These QTLs are located across the chromosomes and provide valuable information on the genes that control the SPP in different populations. In addition, SPP QTLs have been mapped as a single Mendelian factor (Zhang et al., 2006, 2009) and were rarely found on chromosomes 5 and 10 (Thomson et al., 2003; Tan et al., 2008). And these studies showed that the wild rice allele leads to increased or decreased number of SPP. Increase of the grain weight is a method for increasing rice yield. Genes that affect the grain size have been identified in inter-specific crosses (Xiao et al., 1998; Thomson et al., 2003; Li et al., 2004; Aluko et al., 2004; Brondani et al., 2002). In most cases, wild-type alleles were associated with small grain, whereas cultivar alleles were associated with large grains. Usually, grain size is determined by grain length (GL), width, and thickness. These 3 traits are quantitatively inherited under the control of several or many genes. To date, 5 key genes controlling seed size have been isolated in rice: GS3, GW2, qSW5 or GW5, GIF1 and GS5. (Fan et al., 2006; Song et al., 2007; Shomura et al., 2008; Weng et al., 2008; Li et al., 2011). GS3 has a major effect on seed length, whereas qSW5/GW5 and GW2 confer both the seed or grain width (GW) and weight in rice. GIF1 encodes a cell-wall invertase that is required for carbon partitioning during early grain filling, and the over-expression of GIF1 by using its native promoter leads to large grains (Wang et al., 2008). Shomura et al. (2008) found t (...truncated)


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Xiao Luo, Shi-Dong Ji, Ping-Rong Yuan, Hyun-Sook Lee, Dong-Min Kim, Sangshetty Balkunde, Ju-Won Kang, Sang-Nag Ahn. QTL mapping reveals a tight linkage between QTLs for grain weight and panicle spikelet number in rice, Rice, 2013, pp. 33, Volume 6, Issue 1, DOI: 10.1186/1939-8433-6-33