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To develop superior rice varieties with improved yield in most rainfed areas of Asia/Africa, we started an introgression-breeding program for simultaneously improving yield and tolerances of multiple abiotic stresses. Using eight BC1 populations derived from a widely adaptable recipient and eight donors plus three rounds of phenotypic selection, we developed 496 introgression lines (ILs) with significantly higher yield under drought, salt and/or non-stress conditions in 5 years. Six new varieties were released in the Philippines and Pakistan and many more are being evaluated in multi-location yield trials for releasing in several countries. Marker-facilitated genetic characterization revealed three interesting aspects of the breeding procedure: (1) the donor introgression pattern in specific BC populations was characteristic; (2) introgression frequency in different genomic regions varied considerably, resulting primarily from strong selection for the target traits; and (3) significantly lower heterozygosity was observed in BC progenies selected for drought and salinity tolerance. Applying strong phenotypic selection under abiotic stresses in early segregating generations has major advantages for not only improving multiple abiotic stress tolerance but also achieving quicker homozygosity in early generations. This breeding procedure can be easily adopted by small breeding programs in developing countries to develop high-yielding varieties tolerant of abiotic stresses. The large set of trait-specific ILs can be used for genetic mapping of genes/QTL that affect target and non-target traits and for efficient varietal development by designed QTL pyramiding and genomics-based recurrent selection in our Green Super Rice breeding technology.

The power of selection and phenotypic plasticity of seven rice grain yield (GY) traits was dissected using DNA markers and 226 Minghui86 introgression lines (ILs) phenotyped across four contrast environments of long‐day versus short‐day and drought versus irrigated conditions. Linkage mapping identified 77 main‐effect quantitative trait loci (QTLs) plus 15 groups of epistatic QTLs affecting the GY traits. By characterizing genomic introgression patterns of the donor alleles in ILs selected for high‐ and low‐trait values based on replicated progeny testing across each of the four environments and for high‐ and low‐GY across nine different environmental scenarios, 246 QTLs affecting the seven yield traits were identified. Genetic drag from tight repulsive linkage of genes with opposite effects on the same traits was detected in 45 cases involving 90 (35.8%) QTLs, indicating its wide presence in superior Chinese hybrid parents. The demonstrated selective introgression strategy, including the developed ILs plus the genetic information on the associations of introgressed donor alleles with the yield traits in the ILs would provide a useful platform for future breeding by design. [ABSTRACT FROM AUTHOR]

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]