Yu-Chien Tseng

Sorghum (Sorghum bicolor) exhibits drought resistance and environmental adaptability, making it a crucial cereal crop for semi-arid regions. It has a wide range of uses, including as food, feed, brooms, alcohol production, and bioethanol. In particular, Taiwan imports nearly 50,000 tons of sorghum annually, primarily for the production of sorghum liquor. However, the ideal raw material for high-quality sorghum liquor is waxy sorghum, and not all sorghum varieties imported or promoted in Taiwan are of this waxy type. Consequently, there is a shortage of sufficient waxy sorghum raw materials to meet the demands of the Taiwan market. The occurrence of waxy sorghum (wx) is caused by the mutation of granule-bound starch synthase I (GBBS I), and there are currently several known types of mutants, carrying different wx^a, wx^b, and wx^c waxy alleles. Among them, wx^c is a novel mutation type, and in native sorghum in Taiwan, individuals with the waxy allele wx^c have been found. The three-line method is a commonly used breeding strategy, which simplifies the process of emasculation to obtain hybrid F₁ offspring. In this study, imported sorghum variety Liangnuo No.1 (with male sterility), native glutinous sorghum variety SB6 from Taiwan (carrying the wx^c waxy allele), and sorghum reference genome variety BTx623 were used as research materials. The goal was to use the three-line method to produce waxy sorghums, including the male sterile line (A-line), male sterile maintenance line (B-line), and fertility-restoring line (R-line). The breeding results showed that by using backcross breeding, molecular-assisted selection, and traditional field selection methods, high-quality three-line materials (A-, B-, R-lines, named CNA1, CNB1 CNR1, respectively) and F₁ hybrid (CNH1) with favorable agronomic traits and yield quality were successfully obtained.

Rice (Oryza sativa L.) is an important crop worldwide. Functional rice has exhibited health benefits. The aim of this study was to use marker-assisted selection (MAS) to introgress two genes, GE (giant embryo) and OsALDH7 (aldehyde dehydrogenase, golden-like endosperm) into colored rice and obtain high yield functional rice. CNY103108 and CNY103107 are two rice lines with golden-like endosperms and giant embryos. They were used as the donor parents. CNY922401, an elite purple waxy rice line, and TNGSW26, an indica red waxy rice cultivar were used as the recurrent parents. Foreground selection of the progenies was completed using functional markers for GE and OsALDH7, and background selection was completed using molecular markers to recover the background of the recurrent parents. MAS results showed a purple functional rice population (PFR) (CNY922401/CNY103108), with the recovery rate of the recurrent parental genome as 91.3%, and a red functional rice population (RFR) (TNGSW26/CNY103107) with the recovery as 89.8%. After five-season yield trials and several antioxidant activities analyses, PFR32 and RFR13 lines, which have similar yields and antioxidant activities, were selected as the recurrent parents with a golden-like endosperm and a giant embryo. For a biofortification purpose, they can become valuable products and be adapted to the current agricultural community.

The cultivated peanut ( Arachis hypogaea L.) is an important oil crop but has a narrow genetic diversity. Molecular markers can be used to probe the genetic diversity of various germplasm. In this study, the restriction site associated DNA (RAD) approach was utilized to sequence 31 accessions of Taiwanese peanut germplasm, leading to the identification of a total of 17,610 single nucleotide polymorphisms (SNPs). The origin of these 31 accessions is contrasted so the global subset (n = 17) has greater genetic diversity than the local subset (n = 14). Concerning botanical varieties, the var. fastigiata subset has greater genetic diversity than the other two subsets of var. vulgaris and var. hypogaea , suggesting that novel genetic resources should be introduced into breeding programs to enhance genetic diversity. Principal component analysis (PCA) using genotyping data separated the 31 accessions into three clusters largely according to the botanical varieties, consistent with the PCA result for 282 accessions genotyped by 14 kompetitive allele-specific PCR (KASP) markers developed in this study. The SNP markers identified in this work not only revealed the genetic relationship and population structure of current germplasm in Taiwan, but also offer an efficient tool for breeding and further genetic applications.

Cultivated peanut (Arachis hypogaea L.) is an important crop worldwide, and peanut germplasm is an important genetic resource for peanut breeding. The two-season cropping system is common in tropical and subtropical regions, which are the main peanut production areas. The weather in the two cropping seasons is usually distinct and makes germplasm evaluation challenging. In this study, random stratified sampling based on market type was applied to build a core collection. Comparisons between the original entire collection and core collection were conducted. Two seasons field trials were performed with additional three seasons rust resistance evaluation trials. Principal component analysis and genotype-by-trait biplots were utilized as selection tools. Which-won-where/what and stability plot relationships were determined to provide breeders with an easy and efficient method for selection. Rust resistance simple sequence repeat and single nucleotide polymorphism markers were used to screen the germplasm. Some resistant accessions showed susceptible phenotypes, indicating that under Taiwan’s environment, the favored rust physiological races are different from those of other areas. Some potential rust resistance lines were discovered and validated, which can survive under variable weather conditions in a two-season cropping system. A set of markers was developed for utilization for rust resistance screening in Taiwan.

Tainung82 (TNG82) is one of the most popular japonica varieties in Taiwan due to its relatively high yield and grain quality, however, TNG82 is susceptible to bacterial blight (BB) disease. The most economical and eco-friendly way to control BB disease in japonica is through the utilization of varieties that are resistant to the disease. In order to improve TNG82’s resistance to BB disease, five bacterial blight resistance genes (Xa4, xa5, Xa7, xa13 and Xa21) were derived from a donor parent, IRBB66 and transferred into TNG82 via marker-assisted backcrossing breeding. Five BB-resistant gene-linked markers were integrated into the backcross breeding program in order to identify individuals possessing the five identified BB-resistant genes (Xa4, xa5, Xa7, xa13 and Xa21). The polymorphic markers between the donor and recurrent parent were used for background selection. Plants having maximum contribution from the recurrent parent genome were selected in each generation and crossed with the recipient parent. Selected BC₃F₁ plants were selfed in order to generate homozygous BC₃F₂ plants. Nine pyramided plants, possessing all five BB-resistant genes, were obtained. These individuals displayed a high level of resistance against the BB strain, XF89-b. Different BB gene pyramiding lines were also inoculated against the BB pathogen, resulting in more than three gene pyramided lines that exhibited high levels of resistance. The five identified BB gene pyramided lines exhibited yield levels and other desirable agronomic traits, including grain quality and palatability, consistent with TNG82. Bacterial blight-resistant lines possessing the five identified BB genes exhibited not only higher levels of resistance to the disease, but also greater yield levels and grain quality. Pyramiding multiple genes with potential characteristics into a single genotype through marker-assisted selection can improve the efficiency of generating new crop varieties exhibiting disease resistance, as well as other desirable traits.

Seed maturity in peanut (Arachis hypogaea L.) determines economic return to a producer because of its impact on seed weight (yield), and critically influences seed vigor and other quality characteristics. During seed development, the inner mesocarp layer of the pericarp (hull) transitions in color from white to black as the seed matures. The maturity assessment process involves the removal of the exocarp of the hull and visually categorizing the mesocarp color into varying color classes from immature (white, yellow, orange) to mature (brown, and black). This visual color classification is time consuming because the exocarp must be manually removed. In addition, the visual classification process involves human assessment of colors, which leads to large variability of color classification from observer to observer. A more objective, digital imaging approach to peanut maturity is needed, optimally without the requirement of removal of the hull's exocarp. This study examined the use of a hyperspectral imaging (HSI) process to determine pod maturity with intact pericarps. The HSI method leveraged spectral differences between mature and immature pods within a classification algorithm to identify the mature and immature pods. The results showed a high classification accuracy with consistency using samples from different years and cultivars. In addition, the proposed method was capable of estimating a continuous-valued, pixel-level maturity value for individual peanut pods, allowing for a valuable tool that can be utilized in seed quality research. This new method solves issues of labor intensity and subjective error that all current methods of peanut maturity determination have.

Genetic data for traditional Taiwanese (Formosan) agriculture is essential for tracing the origins on the East Asian mainland of the Austronesian language family, whose homeland is generally placed in Taiwan. Three main models for the origins of the Taiwanese Neolithic have been proposed: origins in coastal north China (Shandong); in coastal central China (Yangtze Valley), and in coastal south China. A combination of linguistic and agricultural evidence helps resolve this controversial issue. We report on botanically informed linguistic fieldwork of the agricultural vocabulary of Formosan aborigines, which converges with earlier findings in archaeology, genetics and historical linguistics to assign a lesser role for rice than was earlier thought, and a more important one for the millets. We next present the results of an investigation of domestication genes in a collection of traditional rice landraces maintained by the Formosan aborigines over a hundred years ago. The genes controlling awn length, shattering, caryopsis color, plant and panicle shapes contain the same mutated sequences as modern rice varieties everywhere else in the world, arguing against an independent domestication in south China or Taiwan. Early and traditional Formosan agriculture was based on foxtail millet, broomcorn millet and rice. We trace this suite of cereals to northeastern China in the period 6000–5000 BCE and argue, following earlier proposals, that the precursors of the Austronesians, expanded south along the coast from Shandong after c. 5000 BCE to reach northwest Taiwan in the second half of the 4th millennium BCE. This expansion introduced to Taiwan a mixed farming, fishing and intertidal foraging subsistence strategy; domesticated foxtail millet, broomcorn millet and japonica rice; a belief in the sacredness of foxtail millet; ritual ablation of the upper incisors in adolescents of both sexes; domesticated dogs; and a technological package including inter alia houses, nautical technology, and loom weaving. We suggest that the pre-Austronesians expanded south along the coast from that region after c. 5000 BCE to reach northwest Taiwan in the second half of the 4th millennium BCE.

Spotted wilt, caused by tomato spotted wilt virus (TSWV), is a major disease of peanut (Arachis hypogaea) in the south‐eastern United States. Cultivar resistance is the most important factor in disease control. However, spotted wilt resistance in current cultivars still carries risk in the absence of other practices when disease is severe. In contrast, a newly developed cultivar, Florida‐EP™ “113,” has demonstrated excellent resistance even when spotted wilt is severe. Information on heritability of this resistance can help breeders better utilize it in breeding. F₂‐derived populations from the cross Florida‐EP™ “113”/Georgia Valencia were developed and tested in field experiments in Florida from 2012 to 2014. Disease symptoms were evaluated visually, and the frequency of TSWV infection was measured by ImmunoStrip^®. Heritability estimated from ImmunoStrip^® was higher (0.66) compared to visual ratings (0.48). Genetic correlations among evaluation methods (r_A = 0.92–0.99) and environments (r_B = 0.86–0.99) were high. These results indicate that resistance in Florida‐EP™ “113” is highly heritable and that selection in a high disease risk environment is feasible without significant erosion of genetic gain.