Elite crop varieties usually fix alleles that occur at low frequencies within non-elite gene pools. Dissecting these alleles for desirable agronomic traits can be accomplished by comparing the genomes of elite varieties with those from non-elite populations. Here we deep-sequence six elite rice varieties and use two large control panels to identify elite variety tag single-nucleotide polymorphism alleles (ETASs). Guided by this preliminary analysis, we comprehensively characterize one protein-altering ETAS in the 9-cis-epoxycarotenoid dioxygenase gene of the IRAT104 upland rice variety. This allele displays a drastic frequency difference between upland and irrigated rice, and a selective sweep is observed around this allele. Functional analysis indicates that in upland rice, this allele is associated with significantly higher abscisic acid levels and denser lateral roots, suggesting its association with upland rice suitability. This report provides a potential strategy to mine rare, agronomically important alleles.

Two species in genus Oryza, O. glaberrima and O. glumaepatula, are valuable and potential sources of useful genes of interest for rice improvement. However, the hybrid sterility between O. sativa and these two species is a main reproduction barrier when transferring the favorable traits/genes to O. sativa. To overcome it, the nature of hybrid sterility should be understood further. The objective in the report is to map a new hybrid sterility gene as a Mendelian factor from O. glaberrima and analyze the co-linear of hybrid sterility S loci between O. glaberrima and O. glumaepatula via comparative mapping approach. A BC 2 F 2 population derived from a single semi-sterility plant of BC 2 F 1 of WAB56-104/ WAB450-11-1-2-P41-HB (WAB450-6) //WAB56-104///WAB56-104 was employed to map this pollen killer in O. glaberrima since WAB450-6 is a progeny of interspecific hybrid between O. sativa and O. glaberrima. A new pollen killer locus, S29(t) in O. glaberrima, was identified and mapped to interval between SSR marker RM7033 (1.1 cM) and RM7562 (1.3 cM) on rice chromosome 2. Comparative mapping indicated that S29(t) closely corresponded to S22 which is also a pollen killer gene in O. glumaepatula and is tightly linked with RFLP marker S910 on the short arm of rice chromosome 2. The good co-linear between S29(t) and S22 implied that there might exist common (orthologous) hybrid sterility loci controlled the reproduction barrier among AA genome species of genus Oryza, which will contribute significantly to our understanding of speciation and operation of hybrid sterility between O. sativa and its AA genome relatives.

Hybrid sterility hinders the transfer of useful traits between Oryza sativa and O. glaberrima. In order to further understand the nature of interspecific hybrid sterility between these two species, a strategy of multi-donors was used to elucidate the range of interspecific hybrid sterility in this study. Fifty-nine accessions of O. glaberrima were used as female parents for hybridization with japonica cultivar Dianjingyou 1, after several backcrossings using Dianjingyou 1 as the recurrent parent and 135 BC6F1 sterile plants were selected for genotyping and deducing hybrid sterility QTLs. BC6F1 plants containing heterozygous target markers were selected and used to raise BC7F1 mapping populations for QTL confirmation and as a result, one locus for gamete elimination on chromosome 1 and two loci for pollen sterility on chromosome 4 and 12, which were distinguished from previous reports, were confirmed and designated as S37(t), S38(t) and S39(t), respectively. These results will be valuable for understanding the range of interspecific hybrid sterility, cloning these genes and improving rice breeding through gene introgression.

To further understand the nature of hybrid sterility between Oryza sativa and Oryza glaberrima, quantitative trait loci (QTL) controlling hybrid sterility between the two cultivated rice species were detected in BC 1 F 1 and advanced backcross populations. A genetic map was constructed using the BC 1 F 1 population derived from a cross between WAB450-16, an O. sativa cultivar, and CG14, an O. glaberrima cultivar. Seven main-eVect QTLs for pollen and spikelet sterility were detected in the BC 1 F 1 . Forty-four sterility NILs (BC 6 F 1 ) were developed via successive backcrosses using pollen sterility plants as female and WAB450-16 as the recurrent parent. Seven NILs, in which the target QTL regions were heterozygous while the other QTL regions as well as most of the reminder of the genome were homozygous for the WAB450-16 allele, were selected as the QTL identiWcation materials. BC 7 F 1 for the seven NILs showed a continuous variation in pollen and spikelet fertility. The four identiWed pollen sterility QTLs were located one each on chromosomes 1, 3, 7 and 7. Pollen sterility loci qSS-3 and qSS-7a were on chromosomes 3 and 7, respectively, which coincides with the previously identiWed S19, and S20, while loci qSS-1 and qSS-7b on chromosomes 1 and 7L appear distinct from all previously reported loci. An epistatic interaction controlling the hybrid sterility was detected between qSS-1 and qSS-7a.

Hybrid sterility is a serious barrier in the utilization of wild rice for breeding, but little is known regarding hybrid sterility between the cultivated rice, Oryza sativa, and its wild relative, O. longistaminata. In order to understand further the nature of interspecific hybrid sterility, pollen and spikelet fertility were investigated in two BC 7 F 2 populations derived from a semisterile individual of BC 5 F 1 between Oryza sativa L. and O. longistaminata. One main-effect QTL for pollen and spikelet fertility qpsf6 was detected on the short arm of chromosome 6 close to RM587, around it favoring O. longistaminata allele was found. Comparing the position and effect with other studies indicated that this QTL coincides with the gamete eliminator, S1. It suggests that there exists an orthologous hybrid sterility locus that controls the reproduction barrier between O. sativa and its AA genome relatives. QTL mapping for plant height was also conducted in one of the BC 7 F 2 populations. One QTL, qph1, was detected on the long arm of chromosomes 1 close to RM6333 and coincides with the semi-dwarf gene, sd-1. These new QTL information will increase the efficiency of cultivar development via interspecific hybridization involving O. longistaminata, and offset the stage for fine mapping of these QTL.