The world-renowned Thai Hom Mali Rice has been the most important aromatic rice originating in Thailand. The aromatic variety was collected from Chachoengsao, a central province, and after pure-line selection, it was officially named as Khao Dawk Mali 105, (KDML105). Because of its superb fragrance and cooking quality, KDML105 has been a model variety for studying genes controlling grain quality and aroma. The aromatic gene was cloned in KDML105, as an amino aldehyde dehydrogenase (AMADH) or better known as BADH2 located on chromosome 8. Later on, all other aromatic rice genes were discovered as allelic to the AMADH. As a selection of local landrace variety found in rainfed areas, the Thai Jasmine rice showed adaptive advantages over improved irrigated rice in less fertile lowland rainfed conditions. Because KDML105 was susceptible to most diseases and insect pests, marker-assisted backcross selection (MABC) was used for the genetic improvement since 2000. After nearly 17 years of MABC for integrating new traits into KDML105, a new generation of KDML105, designated HM84, was developed which maintains the cooking quality and fragrance, and has gained advantages during flash flooding, disease, and insect outbreak.

Background: Pyramiding multiple genes into a desirable genetic background can take years to accomplish. In this paper, a pseudo-backcrossing scheme was designed to shorten the backcrossing cycle needed. PinK3, an aromatic and potentially high-yielding rice variety—although one that is intolerant to flash flooding (Sub) and susceptible to bacterial leaf blight (BB), leaf-neck blast (BL) and the brown planthopper (BPH)—was used as a genetic basis for significant improvements through gene pyramiding.Results: Four resistance donors with five target genes (Sub1A-C, xa5, Xa21, TPSandSSIIa) and three QTLs (qBph3, qBL1 and qBL11) were backcrossed individually using markers into the pseudo-recurrent parent ‘PinK3’ via one cycle of backcrossing followed by two cycles of pseudo-backcrossing and three selfings with rigorous foreground marker-assisted selection. In total, 29 pseudo-backcross inbred lines (BILs) were developed. Genome composition was surveyed using 61 simple sequence repeats (SSRs), 35 of which were located on six carrier chromosomes, with the remainder located on six non-carrier chromosomes. The recurrent genome content (%RGC) and donor genome content (%DGC), which were based on the physical positions of BC₁F₂, ranged from 69.99 to 88.98% and 11.02 to 30.01%, respectively. For the pseudo-BC₃F₃BILs, the %RGC and %DGC ranged from 74.50 to 81.30% and 18.70 to 25.50%, respectively. These results indicated that without direct background selection, no further increases in %RGC were obtained during pseudo-backcrossing, whereas rigorous foreground marker-assisted selection tended to reduce linkage drag during pseudo-backcrossing. The evaluation of new traits in selected pseudo-BC₃F₃BILs indicated significant improvements in resistance to BB, BL, BPH and Sub compared with PinK3, as well as significant improvements in grain yield (21-68%) over the donors, although yield was 7-26% lower than in ‘PinK3’. All pyramided lines were aromatic and exhibited improved starch profiles, rendering them suitable for industrial food applications.Conclusions: Results show that our new pyramiding platform, which is based on marker-assisted pseudo-backcrossing, can fix five target genes and three QTLs into a high-yielding pseudo-recurrent background within seven breeding cycles in four years. This multiple pseudo-backcrossing platform decreases the time required to generate new rice varieties exhibiting complex, durable resistance to biotic and abiotic stresses in backgrounds with desirable qualities.

The development of rice varieties with broad-spectrum resistance to insect pests is the most promising approach for controlling a fast evolving insect pest such as the brown planthopper (BPH). To cope with rapid evolution, discovering new sources of broad-spectrum resistance genes is the ultimate goal. We used a forward genetics approach to identify BPH resistance genes in rice (Oryza sativa L.) using double digest restriction site-associated DNA sequencing (ddRADseq) for quantitative trait loci (QTL)-seq of the backcross inbred lines (BILs) derived from a cross between the BPH-susceptible cultivar KDML105 and BPH-resistant cultivar Rathu Heenati (RH). Two major genomic regions, located between 5.78-7.78 Mb (QBPH4.1) and 15.22-17.22 Mb (QBPH4.2) on rice chromosome 4, showed association with BPH resistance in both pooled BILs and individual highly resistant and susceptible BILs. The two most significant candidate resistance genes located within the QBPH4.1 and QBPH4.2 windows were lectin receptor kinase 3 (OsLecRK3) and sesquiterpene synthase 2 (OsSTPS2), respectively. Functional markers identified in these two genes were used for reverse screening 9323 lines of the fast neutron (FN)-mutagenized population developed from the BPH-susceptible, purple-pigmented, indica cultivar Jao Hom Nin (JHN). Nineteen FN-mutagenized lines (0.24%) carried mutations in the OsLecRK3 and/or OsSTPS2 gene. Among these mutant lines, only one highly resistant line (JHN4) and three moderately resistant lines (JHN09962, JHN12005, and JHN19525) were identified using three active, local BPH populations. The 19 mutant lines together with three randomly selected mutant lines, which did not harbor mutations in the two target genes, were screened further for mutations in six known BPH resistance genes including BPH9, BPH14, BPH18, BPH26, BPH29, and BPH32. Multiple single nucleotide polymorphisms (SNPs) and insertion-deletion (Indel) mutations were identified, which formed gene-specific haplotype patterns (HPs) essential for broad-spectrum resistance to BPH in both BILs and JHN mutant populations. On the one hand, HPs of OsLekRK2-3, OsSTPS2, and BPH32 determined broad-spectrum resistance to BPH among RH-derived BILs. On the other hand, in the JHN mutant population, BPH9 together with seven significant genes on chromosome 4 played a crucial role in BPH resistance.

Consumers’ general preference for white rice over whole grain rice stems from the hardness and low palatability of cooked whole grain rice; however, strong links have been found between consuming a large amount of white rice, leading a sedentary lifestyle, and acquiring type 2 diabetes. This led us to formulate a new breeding goal to improve the softness and palatability of whole grain rice while promoting its nutritional value. In this study, the association between dietary fibre profiles (using an enzymatic method combined with high-performance liquid chromatography) and textural properties of whole grain rice (using a texture analyser) was observed. The results showed that a variation in the ratio of soluble dietary fibre (SDF) and insoluble dietary fibre (IDF) influenced the textural characteristics of cooked whole grain rice; found a strong association between SDF to IDF ratio and hardness (r = −0.74, p < 0.01) or gumminess (r = −0.69, p < 0.01) of cooked whole grain rice, and demonstrated that the SDF to IDF ratio was also moderately correlated with cohesiveness (r = −0.45, p < 0.05), chewiness (r = −0.55, p < 0.01), and adhesiveness (r = 0.45, p < 0.05) of cooked whole grain rice. It is suggested that the SDF to IDF ratio can be used as a biomarker for breeding soft and highly palatable whole grain rice of cultivated tropical indica rice to achieve consumer well-being. Lastly, a simple modified method from the alkaline disintegration test was developed for high-throughput screening of dietary fibre profiles in the whole grain indica rice samples.

The demand for rice varieties with lower amylose content (AC) is increasing in Southeast Asia, primarily due to their desirable texture and cooking qualities. This study presents the development of whole-grain rice lines with low to intermediate glycemic index (GI) and reduced AC. We selected six rice lines for in vivo GI assessment based on their starch properties. We successfully identified two lines with low AC that exhibited low and intermediate GI values, respectively. Our findings indicate that dietary fiber (DF) content may significantly influence rice GI. The selected whole-grain low-GI line showed a higher ratio of soluble dietary fiber (SDF) to insoluble dietary fiber (IDF) compared to control varieties, highlighting SDF’s potential positive role in lowering whole-grain rice’s GI. This study underscores the feasibility of developing rice varieties with desirable agronomic traits, nutritional traits, and culinary attributes, particularly for individuals managing their blood sugar levels. Additionally, we proposed the positive role of starch composition, especially DF content, in modulating the GI of rice. This study reinforces the importance of incorporating starch properties and DF content into rice breeding programs to produce more health-oriented and marketable rice varieties.

The demand for rice varieties with lower amylose content (AC) is increasing in Southeast Asia, primarily due to their desirable texture and cooking qualities. This study presents the development of whole-grain rice lines with low to intermediate glycemic index (GI) and reduced AC. We selected six rice lines for in vivo GI assessment based on their starch properties. We successfully identified two lines with low AC that exhibited low and intermediate GI values, respectively. Our findings indicate that dietary fiber (DF) content may significantly influence rice GI. The selected whole-grain low-GI line showed a higher ratio of soluble dietary fiber (SDF) to insoluble dietary fiber (IDF) compared to control varieties, highlighting SDF's potential positive role in lowering whole-grain rice's GI. This study underscores the feasibility of developing rice varieties with desirable agronomic traits, nutritional traits, and culinary attributes, particularly for individuals managing their blood sugar levels. Additionally, we proposed the positive role of starch composition, especially DF content, in modulating the GI of rice. This study reinforces the importance of incorporating starch properties and DF content into rice breeding programs to produce more health-oriented and marketable rice varieties.