Search

Seedling vigour (SV) is important for direct seeding rice (Oryza sativa L.), especially in a paddy-direct seeding system, but the genetic mechanisms behind the related traits remain largely unknown. Here, we used 744 germplasms, having at least two subsets, for the detection of quantitative trait loci (QTLs) affecting the SV-related traits tiller number, plant height, and aboveground dry weight at three sampling stages, 27, 34, and 41 d after sowing. A joint map based on GAPIT and mrMLM produced a satisfying balance between type I and II errors. In total, 42 QTL regions, containing 18 (42.9%) previously reported overlapping QTL regions and 24 new ones, responsible for SV were detected throughout the genome. Four QTL regions, qSV1a, qSV3e, qSV4c, and qSV7c, were delimited and harboured quantitative trait nucleotides that are responsible for SV-related traits. Favourable haplotype mining for the candidate genes within these four regions, as well as the early SV gene OsGA20ox1, was performed, and the favourable haplotypes were presented with donors from the 3,000 Rice Genome Project. This work provides new information and materials for the future molecular breeding of direct seeding rice, especially in paddy-direct seeding cultivation systems.

Single nucleotide polymorphisms (SNPs) are the most abundant DNA markers in plant genomes. In this study, based on 54,465 SNPs between the genomes of two Indica varieties, Minghui 63 (MH63) and Zhenshan 97 (ZS97) and additional 20,705 SNPs between the MH63 and Nipponbare genomes, we identified and confirmed 1,633 well-distributed SNPs by PCR and Sanger sequencing. From these, a set of 372 SNPs were further selected to analyze the patterns of genetic diversity in 300 representative rice inbred lines from 22 rice growing countries worldwide. Using this set of SNPs, we were able to uncover the well-known Indica- Japonica subspecific differentiation and geographic differentiations within Indica and Japonica. Furthermore, our SNP results revealed some common and contrasting patterns of the haplotype diversity along different rice chromosomes in the Indica and Japonica accessions, which suggest different evolutionary forces possibly acting in specific regions of the rice genome during domestication and evolution of rice. Our results demonstrated that this set of SNPs can be used as anchor SNPs for large scale genotyping in rice molecular breeding research involving Indica- Japonica and Indica-Indica crosses. [ABSTRACT FROM AUTHOR]

Abstract: A novel bacterial blight (BB) resistance gene, Xa23, identified from Oryza rufipogon was introgressed into three popular restorer lines (Minghui63, YR293 and Y1671) for wild abortive cytoplasmic male sterility by marker-assisted backcross breeding approach in combination with artificial inoculation and stringent phenotypic selections. The three derived BB resistant restorer lines (Minghui63–Xa23, YR293–Xa23 and Y1671–Xa23) and their hybrid combinations with Zhenshan97A (Shanyou63–Xa23), NongfengA (Fengyou293–Xa23) and Zhong9A (Zhongyou1671–Xa23) demonstrated similar BB resistance spectrum as the donor parent, CBB23 (B). The newly developed BB resistant restorers and their derived hybrids were identical to their respective original versions for agronomic traits especially under disease free condition. However, under severe disease condition, the three BB resistant restorer lines exhibited significantly higher grain weight and spikelet fertility as compared to the respective original restorer lines thus further resulting in BB resistant hybrids with significantly higher grain yields than their respective popular original hybrids. The results indicated that the Xa23 gene could completely express its dominant broad spectrum resistance in different backgrounds of both restorer and male sterile lines across different growth stages, suggesting its immense breeding value in BB resistance improvement for hybrid rice. Moreover, a reasonable utilization and deployment of Xa23 gene for efficient control of BB disease in hybrid rice production was recommended. [Copyright &y& Elsevier]

Abstract: Expression of quantitative trait locus (QTL) is affected by genetic background (GB) and environment. The GB effect on QTL mapping and QTL by environment interaction for heading date (HD) and plant height (PH) were studied in Beijing and Hainan environments using a large set of reciprocal introgression lines (ILs) derived from a japonica rice (Oryza sativa L.) variety Lemont and an indica variety Teqing. In both environments, the 2 IL populations showed transgressive segregation for HD and PH traits. A total of 16 and 17 main-effect QTLs (M-QTLs) were identified for HD and PH, respectively. Among them, only 5 M-QTLs were detected under the 2 GBs, indicating that the expressions of most M-QTLs are specific to GB. Under both GBs, significant interactions between QTLs and environment responsible for HD were observed at 3 M-QTLs, of which QHd8a antedated heading for 2–3 d in Hainan but delayed heading for 2–3 d in Beijing. Therefore, QHd8a could be considered as an important M-QTL for HD. By comparing with the previous results on QTL mapping using another 7 populations derived from the same parents, a few M-QTLs were found to express stably under different GBs in various environments, such as QHd3, QHd8a, QPh3, and QPh4. These QTLs show applicable potential in marker-assisted breeding for HD and PH in rice. [Copyright &y& Elsevier]