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Purple apiculus is one of the important agronomic traits of rice. Single-segment substitution line (SSSL) W23-07-6-02-14 in the genetic background of an elite rice variety Huajingxian74 (HJX74) with the substituted interval of RM225-RM217-RM253 on the chromosome 6 was found to have purple apiculus (Pa). To map the gene governing Pa, W23-07-6-02-14 was crossed with the recipient HJX74 to develop an F2 secondary segregation population. The ratio of purple apiculus to green apiculus showed a good fit to 3:1 ratio, indicating that Pa was controlled by a major dominant gene. The gene locus for Pa was tentatively designated as Pa-6. Using 430 individuals from the F2 segregation population, the Pa-6 locus was mapped between two SSR markers RM19556 and RM19561 with genetic distances of 0.2 and 0.3 cM, respectively. For fine mapping of the Pa-6 gene, a large F2:3 segregation population of 3890 individuals was developed from F2 heterzygous plants in the RM19556-RM19561 region. Recombinant analyses further mapped the Pa-6 gene locus to an interval of 41.7-kb bounded L02 and RM19561. Sequence analysis of this 41.7-kb region revealed that it contains eleven open reading frames (ORFs), of which, ORF5 is classified as the one that is associated with the C (chromogen for anthocyanin) gene, it was presumed to be the candidate gene for Pa. This result provided a foundation of map-based cloning and function analysis of the Pa-6 gene.

In our previous studies, a single segment substitution line (SSSL) W23-03-8-9-1 with substituted interval of PSM301-PSM306-PSM305-PSM304-RM3894-RM3372-RM569-RM231-RM545 on chromosome 3 has been found to comprise a gene for extremely early heading date. To map this gene, the SSSL W23-03-8-9-1 was crossed with the recipient Huajingxian (HJX74) to develop an F2 segregating population. The distribution of early and late heading plants in this population fitted a segregation ratio of 3: 1, indicating that early heading was controlled by a dominant gene. Using a random sample of 520 individuals from the F2 segregation population, the qHD3-1 locus was mapped between two SSR markers, RM3894 and RM3372, with genetic distances of 1.2 and 1.1 cM, respectively. For fine mapping of qHD3-1, a large F2: 3 segregating population was developed, with 6000 individuals from the F2 plants heterozygous in the RM3894 and RM3372 regions. The analysis of recombinants in the qHD3-1 region put the gene locus into an interval of 29.5 kb flanked by the left marker 3HD8 and the right marker 3HD9. Sequence analysis of this fragment predicted eight open reading frames. One of them, ORF8, with its molecular function predicted to encode ribonuclease III activity and RNA binding, is considered the most interesting candidate gene.

Heading date is one of the importance agronomic traits. A library consisting of 1,123 single segment substitution lines (SSSLs) in the same genetic background of an elite rice variety Huajingxian 74 (HJX74) was evaluated for heading date (HD). From this library, the SSSL W06-26-35-1-5-2 with the substituted interval of PSM152–PSM154–PSM155–RM25–RM547–RM72–RM404 was found having a gene, which performed stable and late heading in the different environments of Shandong and Hainan provinces. To map the gene governing heading date, the SSSL W06-26-35-1-5-2 was crossed with the recipient HJX74 to develop an F2 segregating population. The distribution of late and early heading plants in this population fitted a segregation ratio of 3:1, indicating the late heading was controlled by a dominant gene. The gene locus for heading date was tentatively designated as qHD8-1. Using a random sample of 460 individuals from the F2 population, the qHD8-1 was narrowed down to a region flanking by two SSR markers PSM155 and RM547. For fine mapping of qHD8-1, a large F2:3 segregating population of 3,000 individuals were developed from F2 plants heterozygous in the PSM155–RM547 region. Recombinants analysis further mapped qHD8-1 to an interval of region 26 kb with markers RM22492 and P23 bounded on the left and right sides, respectively. Sequence analysis of this 26-kb fragment revealed that it contains five putative open reading frames, which were regarded as candidates of qHD8-1. These results will be useful in cloning of the qHD8-1 gene.

A library consisting of 1,123 single-segment substitution lines (SSSLs) in the same genetic background of an elite rice variety Huajingxian74 (HJX74) was evaluated for heading date. From this library, the SSSL W05-1-11-5-16-2-5 with the substituted interval of PSM103—RM348-OSR15-PSM382-RM131-RM127—RM280 was found having a gene, which stably performed extreme late heading date which performed stable and late heading in the different environments of Shandong, Guangdong, and Hainan. To map the gene governing heading date, the SSSL W05-1-11-5-16-2-5 was crossed with the recipient HJX74 to develop an F2 segregating population. The distribution of late and early heading plants in this population fitted a segregation ratio of 3:1, indicating the late heading was controlled by a dominant gene. The gene locus for heading date was tentatively designated as qHD4-1. Using a random sample of 460 individuals from the F2 segregation population, the qHD4-1 locus was mapped between two SSR markers RM3335 and RM17572, with genetic distances of 0.1 and 0.2 cM, respectively. For fine mapping of qHD4-1, a large F2:3 segregating population of 3,000 individuals were developed from F2 plants heterozygous in the RM3335-RM17572 region. Recombinants analyses further mapped qHD4-1 to an interval of 20.7-kb-bounded WB05 and the WB06. Sequence analysis of this 20.7-kb region revealed that it contains three open reading frames (ORFs), encoding wall-associated receptor kinase-like 5, putative F-box domain containing protein, and putative arogenate/prephenate dehydratase. Of them, ORF1, predicting to encode serine/threonine kinase, is considered the most likely as the candidate gene. The genetic and physical map of the qHD4-1 locus will be very useful in molecular cloning of the qHD4-1gene.

A library consisting of 1123 single segment substitution lines (SSSLs) in the same genetic back-ground of an elite rice variety Huajingxian74 (HJX74) was evaluated for heading date. From this library, two SSSLs, W23-03-8-9-1 and W15-03-1-31, with substitution segments on chromosome 3 and 2, respectively, were found to have significantly different heading date from the recipient HJX74. For genetic dissection and epistatic interaction of quantitative trait loci (QTLs) for heading date in two SSSLs, three secondary SSSLs with smaller substitution segments and genic pyramiding lines (GPLs) were developed from an F2 segregating population of a cross between the two donor SSSLs, W23-03-8-9-1 and W15-03-1-31, using marker-assisted selection (MAS). The QTL analysis revealed that QTL for heading date detected in SSSL W23-03-08-9-1 was genetically dissected into two QTLs, qHD3-1 and qHD3-2, by overlapping mapping. At the same time, one QTL, qHD2-1 in the donor SSSL W15-03-1-31 was also identified. Analysis of GPLs for heading date showed epistatic interactions between qHD3-1 and qHD3-2, between qHD3-1 and qHD2-1, and between qHD3-2 and qHD2-1. These QTLs and epistatic interactions were confirmed in three cropping seasons under different natural daylength conditions, and their physiological functions for heading date were performed.

The fragrance gene plays an important role in high-quality rice varieties and has been widely used in breeding programs. Using a random sample of 370 individuals from an F2 segregating population developed from a cross between a japonica rice variety 9407 with fragrant flavor and an indica variety IRBB60, the fgr locus was mapped on chromosome 8 between SSR markers, PSM465 and RM1109, with genetic distances of 0.3 cM and 0.1 cM to respective markers. These mapping efforts confirmed the previous mapping results. A large F3 mapping population with 7300 individuals was then developed from F2 plants, in which a small chromosomal region defined by the SSR markers, PSM465 and RM1109, was heterozygous. The analysis of recombinants in the fgr region anchored the gene locus to an interval of 28 kb flanked by the left marker NS9 and the right marker L06. Sequence analysis of this fragment predicted three open reading frames encoding putative 3-methylcrotonyl-CoA carboxylase, putative isoleucyl-tRNA synthetase, and betaine aldehyde dehydrogenase (BADH2). The latter was presumed to be the candidate gene for fragrance. This result will be very useful in molecular cloning of the fgr gene and marker-assisted transfer of the fgr gene in rice breeding programs.