Jose E. Hernandez

Genome-Wide Association Mapping for Yield and Other Agronomic Traits in an Elite Breeding Population of Tropical Rice (Oryza sativa)

Genome-wide association mapping studies (GWAS) are frequently used to detect QTL in diverse collections of crop germplasm, based on historic recombination events and linkage disequilibrium across the genome. Generally, diversity panels genotyped with high density SNP panels are utilized in order to assay a wide range of alleles and haplotypes and to monitor recombination breakpoints across the genome. By contrast, GWAS have not generally been performed in breeding populations. In this study we performed association mapping for 19 agronomic traits including yield and yield components in a breeding population of elite irrigated tropical rice breeding lines so that the results would be more directly applicable to breeding than those from a diversity panel. The population was genotyped with 71,710 SNPs using genotyping-by-sequencing (GBS), and GWAS performed with the explicit goal of expediting selection in the breeding program. Using this breeding panel we identified 52 QTL for 11 agronomic traits, including large effect QTLs for flowering time and grain length/grain width/grain-length-breadth ratio. We also identified haplotypes that can be used to select plants in our population for short stature (plant height), early flowering time, and high yield, and thus demonstrate the utility of association mapping in breeding populations for informing breeding decisions. We conclude by exploring how the newly identified significant SNPs and insights into the genetic architecture of these quantitative traits can be leveraged to build genomic-assisted selection models.

Identification of QTLs for Drought-Related Traits in Alien Introgression Lines Derived from Crosses of Rice (Oryza sativa cv. IR64) × O. glaberrima under Lowland Moisture Stress

Drought is a major abiotic stress that limits rice productivity in rain-fed and upland ecosystems. African rice, Oryza glaberrima, has low yields but is tolerant to drought and other stresses. We evaluated 513 BC2F3 progenies from alien introgression lines (AILs) that were derived from crosses of Oryza sativa (IR64) × O. glaberrima. They were assessed for yield and other traits when grown under drought at two locations. Such conditions reduced grain production by 59% compared with the recurrent parent (IR64). However, 33 AILs had higher yields, thus demonstrating their potential as genetic material for transferring drought-related traits from O. glaberrima to O. sativa. A set of 200 AILs was selectively genotyped with 173 simple sequence repeat and sequenced tagged site markers. Molecular analysis showed that a mean of 4.5% of the O. glaberrima genome was introgressed in BC2F3 AILs. Our analysis revealed 33 quantitative trait loci (QTLs; including 10 novel) for different traits. O. glaberrima contributed 50% of the alleles to those newly identified QTLs, with one for grain yield per plant (ypp9.1) being new. A QTL at RM208 on chromosome 2 positively affected yield under stress, accounting for 22% of the genetic variation. Our identification of drought-related QTLs for yield and yield components will be useful to future research efforts in marker-assisted selection.

Exploiting the Genomic Diversity of Rice (Oryza sativa L.): SNP-Typing in 11 Early-Backcross Introgression-Breeding Populations

This study demonstrates genotyping-by-sequencing-based single-nucleotide polymorphism (SNP)-typing in 11 early-backcross introgression populations of rice (at BC1F5), comprising a set of 564 diverse introgression lines and 12 parents. Sequencing using 10 Ion Proton runs generated a total of ∼943.4 million raw reads, out of which ∼881.6 million reads remained after trimming for low-quality bases. After alignment, 794,297 polymorphic SNPs were identified, and filtering resulted in LMD50 SNPs (low missing data, with each SNP, genotyped in at least 50% of the samples) for each sub-population. Every data point was supported by actual sequencing data without any imputation, eliminating imputation-induced errors in SNP calling. Genotyping substantiated the impacts of novel breeding strategy revealing: (a) the donor introgression patterns in ILs were characteristic with variable introgression frequency in different genomic regions, attributed mainly to stringent selection under abiotic stress and (b) considerably lower heterozygosity was observed in ILs. Functional annotation revealed 426 non-synonymous deleterious SNPs present in 102 loci with a range of 1–4 SNPs per locus and 120 novel SNPs. SNP-typing this diversity panel will further assist in the development of markers supporting genomic applications in molecular breeding programs.

Developing Green Super Rice Varieties with High Nutrient Use Efficiency by Phenotypic Selection Under Varied Nutrient Conditions

To develop green super rice varieties with high and stable yields under the rainfed conditions and improved nutrient use efficiency (NuUE), a modified backcross (BC) breeding approach was adopted using a high yielding and widely adaptable Xian variety, WTR1, as the recipient and a Geng variety, HAN, as the donor. Starting from the BC1F2 generation, the BC population had gone through one generation of selection under the IG, LI and RF conditions, followed by consecutive four generations of screening and selection for high GY under six different nutrient conditions, leading to the development of 230 BC1F6 introgression lines (ILs). The final evaluation of the 230 ILs under the six nutrient conditions identified many ILs with improved yields under various combinations of nutrient deficient conditions, including 12 promising lines that had significantly improved NuUE under two or more nutrient deficiency conditions. Our results demonstrated an efficient inter-subspecific BC breeding procedure with first round selection under the rainfed-drought condition followed by four generations of progeny testing for yield performances under six different nutrient conditions. The promising ILs were studied under replicated yield trials under 75N and -NPK conditions for developing high yield rice varieties with improved NuUE. Our results indicated that NuUE in rice was controlled by complex genetic and physiological mechanisms and the developed ILs provided useful materials for genetic and molecular dissection of NuUE in rice.

Molecular Genetics and Breeding for Nutrient Use Efficiency in Rice

In the coming decades, rice production needs to be carried out sustainably to keep the balance between profitability margins and essential resource input costs. Many fertilizers, such as N, depend primarily on fossil fuels, whereas P comes from rock phosphates. How long these reserves will last and sustain agriculture remains to be seen. Therefore, current agricultural food production under such conditions remains an enormous and colossal challenge. Researchers have been trying to identify nutrient use-efficient varieties over the past few decades with limited success. The concept of nutrient use efficiency is being revisited to understand the molecular genetic basis, while much of it is not entirely understood yet. However, significant achievements have recently been observed at the molecular level in nitrogen and phosphorus use efficiency. Breeding teams are trying to incorporate these valuable QTLs and genes into their rice breeding programs. In this review, we seek to identify the achievements and the progress made so far in the fields of genetics, molecular breeding and biotechnology, especially for nutrient use efficiency in rice.

Cytogenetic analysis of five recommended and released Philippine varieties of sugarcane (Saccharum officinarum L.) and their parentals

Abstract Meiotic chromosomal behavior of five recommended and released Philippine varieties of sugarcane and their parents, namely VMC 95-09 (Q 90 × Unidentified), PSR 97-45 (VMC 74-292 × CP 72-1312), PSR 00-343 (VMC 84-947 × Unidentified), PSR 00-161 (VMC 86-550 × VMC 87-599), and PSR 00-34 (VMC 84-194 × PHIL 89-43) were characterized and analyzed. Samples were collected from the tassel source of Philippine Sugar Research Institute Foundation Inc. (PHILSURIN) located in Negros Occidental, Philippines. Gametic number for each variety was determined at diakinesis and at least 50 cells per meiotic stage was analyzed. All varieties exhibited chromosome mosaicism at diakinesis with n = 40–60. Chromosome clumping was observed at diakinesis of Q 90 (68%), CP 72-1312 (35%), and PSR 97-45 (22%) pollen mother cells. High frequency of bivalent formation (68–100%) was observed, both in parents and hybrids, indicating that chromosome pairing is autosyndetic. Irregularities at meiosis were also observed at high frequencies both in parents and hybrids. Multiple metaphase I plate, non-congression, and laggards were observed at meiosis I and meiosis II. Chromosome contribution of parents to each hybrid was determined based on gametic chromosome number of the parents and their meiotic behavior. Results of this study can be used in identifying best hybrids that can be utilized in an inter or intra-species hybridization to produce better performing sugarcane varieties.