Fine mapping of a grain weight quantitative trait locus, qGW6, using near isogenic lines derived from Oryza rufipogon IRGC105491 and Oryza sativa cultivar MR219

Abstract

ABSTRACT. Grain weight is a major component of rice grain yield and is controlled by quantitative trait loci. Previously, a rice grain weight quantitative trait locus (qGW6) was detected near marker RM587 on chromosome 6 in a backcross population (BC 2 F 2 ) derived from a cross between Oryza rufipogon IRGC105491 and O. sativa cv. MR219. Using a BC 2 F 5 population, qGW6 was validated and mapped to a region of 4.8 cM (1.2 Mb) in the interval between RM508 and RM588. Fine mapping using a series of BC 4 F 3 near isogenic lines further narrowed the interval containing qGW6 to 88 kb between markers RM19268 and RM19271.1. According to the Duncan multiple range test, 8 BC 4 F 4 near isogenic lines had significantly higher 100-grain weight (4.8 to 7.5% over MR219) than their recurrent parent, MR219 (P < 0.05). According to the rice genome automated annotation database, there are 20 predicted genes in the 88-kb target region, and 9 of them have known functions. Among the genes with known functions in the target region, in silico gene expression analysis showed that 9 were differentially expressed during the seed development stage(s) from gene expression series GSE6893; however, only 3 of them have known functions. These candidates provide targets for further characterization of qGW6, which will assist in understanding the genetic control of grain weight in rice.

Fine mapping and candidate gene analysis of Brtri1, a gene controlling trichome development in Chinese cabbage (Brassica rapa L. ssp pekinensis)

“…One gene reported from Chinese cabbage, Bra009770, the homolog of TTG1 on chromosome A06, regulates trichome development and the seed coat color (Zhang et al, 2009). Map-based cloning is one of the most effective ways to isolate genes controlling important agronomic traits (Wei et al, 2013;Ngu et al, 2014;Zou et al, 2016). In our paper, we attempted to clone the gene controlling trichome development in Chinese cabbage using this method.…”

Genomics of crop wild relatives: expanding the gene pool for crop improvement

“…The wild relatives of rice have been extensively studied as sources of genetic diversity for rice improvement. Oryza nivara (Gaikwad et al ., ; Swamy et al ., ) and O. rufipogon (Fu et al ., ; Luo et al ., ; Ngu et al ., ; Thalapati et al ., ) have been used to source novel yield traits. New sources of wild rice germplasm have recently been identified (Brozynska et al ., ; Figure c).…”

Genetic Dissection of Grain Nutritional Traits and Leaf Blight Resistance in Rice

“…Additionally, pigmented rice cultivars, with red, purple, black, brown and yellow kernels, are still grown in some areas in Asia because of their nutritional and medicinal value or as part of traditional cultural practices [22,23,24,25]. This germplasm can be a good source of valuable genes/quantitative trait locis (QTLs) for various nutrition, grain quality, and pest and disease resistance traits for rice breeding programs [4,26,27,28,29,30,31]. Several studies on the characterization of colored rice for different antioxidant compounds, vitamins, and minerals have shown wide variations and these accessions were found to have 3- to 4-fold higher nutrient content than modern rice varieties [32,33,34,35].…”

“…Traditional rice varieties often possess beneficial QTLs or genes for plant improvement that are not available in current cultivated mega-varieties. Several useful QTLs in traditional varieties were identified and used by introgression or pyramiding into cultivars to improve agronomic performance [4,26,27,28,29,30,31]. Understanding the genetic basis of complex traits through the identification of major-effect QTLs/genes, and their application through maker-assisted breeding, is an attractive option to develop nutritious rice varieties.…”