IntroductionExploring natural genetic variation to facilitate breeding of improved rice seedling cold tolerance will allow the crop to be planted earlier in the growing season, taking advantage of spring rainfall and decreasing exposure to high summer nighttime temperatures, which reduce grain quality.MethodsTo uncover genomic regions in rice that manage cold stress tolerance response mechanisms in the cold-sensitive aus (AUS) and the relatively cold-tolerant tropical japonica (TRJ) subpopulations, and to identify cold tolerance genes, AUS and TRJ recombinant inbred line populations developed from crosses between cold-tolerant and cold-sensitive parents were used for quantitative trait locus (QTL) mapping of two traits: degree of membrane damage after 1 week of cold exposure, quantified as percent electrolyte leakage (EL), and percent low-temperature seedling survivability (LTSS) after 1 week of recovery growth.Results and discussionThirteen subpopulation-specfic QTL were revealed: three EL and four LTSS QTL for AUS, and two EL and four LTSS QTL for TRJ, with no overlap between AUS and TRJ QTL. Only two AUS QTL overlapped with regions previously identified by our AUS × temperate japonica biparental mapping, further confirming the discovery of subpopulation-specific QTL. Based on high-impact genomic differences between the cold-tolerant and cold-sensitive parents, 35 cold tolerance candidate genes were identified—23 in AUS and 12 in TRJ—of which about 50% encode proteins involved in signal transduction and protein homeostasis processes. Although most QTL showed that alleles from cold-tolerant parents improved the two cold tolerance traits, alleles from cold-sensitive parents enhanced these traits at several other QTL. Therefore, alleles from both cold-tolerant and cold-sensitive parents can be used in breeding efforts to generate AUS and TRJ lines with better cold tolerance potential than their respective cold-tolerant parents.

Rice is a globally important crop and is particularly efficient at assimilating arsenic (As). Identifying QTLs and genes associated with grain As is essential for breeding low-As rice cultivars. In this study, data on As accumulation in grains of Rice Diversity Panel 1 in five field environments at four diverse geographic sites were reanalyzed to compare genome-wide association (GWA) methods. Two single-locus (EMMAX for single trait and GEMMA for multi-experiments) and six multi-locus (FASTmrEMMA, ISIS EM-BLASSO, mrMLM, pKWmEB, pLARmEB, and FASTmrMLM) GWA methods were used. A total of 90 and 111 QTLs were detected using EMMAX and GEMMA, respectively. A total of 2, 11, 12, 19, 23, and 25 QTNs were identified by FASTmrEMMA, ISIS EM-BLASSO, mrMLM, pKWmEB, pLARmEB, and FASTmrMLM, respectively. Among these, 22 QTLs/QTNs were co-detected by single-locus and multi-locus GWAS methods. From these QTLs/QTNs, a total of 10 candidate genes were identified. Analysis of the haplotype variants of one candidate genes, OsABCC1, and one cluster of the plasma membrane intrinsic proteins genes revealed that a greater than 10% reduction in grain As could be achieved. The QTLs/QTNs and candidate genes identified give insight into the molecular mechanisms regulating As accumulation in rice and serve as breeding targets for developing low grain As rice cultivars.

The two varietal groups of cultivated rice (Oryza sativa) are Indica and Japonica. Ancestral species O. rufipogon and O. nivara, collectively identified as the Oryza rufipogon species complex (ORSC), represent an underutilized resource for rice improvement. To make the ORSC genepool more accessible for breeding, three genotypically and phenotypically diverse ORSC accessions were selected as donors to develop chromosome segment substitution line (CSSL) libraries from crosses with IR64, an indica long grain grown in South and Southeast Asia, and Cybonnet, a U.S. tropical japonica long grain. The Cybonnet (Cyb) x OrA (O. rufipogon, NIAS W1944) CSSL Library (Reg. no. MP-11, NSL 551190 MAP) and IR64 x OrA (O. rufipogon, NIAS W1944) CSSL Library (Reg. no. MP-14, NSL 551377 MAP) used an ORSC donor from China, Cybonnet (Cyb) x OrB (O. nivara, IRGC106148) CSSL Library (Reg. no. MP-12, NSL 551297 MAP) and IR64 x OrB (O. nivara, IRGC106148) CSSL Library (Reg. no. MP-15, NSL 551378 MAP) an ORSC donor from Laos, and Cybonnet (Cyb) x OrC (O. rufipogon, IRGC105567) CSSL Library (Reg. no. MP-13, NSL 551376 MAP) and IR64 x OrC (O. rufipogon, IRGC105567) CSSL Library (Reg. no. MP-16, NSL 551379 MAP) an ORSC donor from Indonesia. The libraries were genotyped with an Infinium 7K array for rice. Previously, Cybonnet and 212 of the 216 Cybonnet CSSLs from the three libraries were evaluated in replicated field studies for six agronomic, six panicle architecture, and eight seed traits. Similarly, IR64 and 218 IR64 CSSLs from three libraries were grown in the greenhouse and characterized for six agronomic traits, panicle type and length, and four seed traits. Awn presence and culm color were noted for all CSSLs with three underlying genes identified. Of the 28 candidate genes identified by substitution mapping in the Cybonnet libraries, 11 were validated for the same traits phenotyped in the IR64 libraries. Phenotypes of CSSLs with ORSC introgressions that included the LK3, Waxy, ALK, and Pita genes validated the ORSC allele for these genes. These six CSSL libraries are a unique resource for researchers to discover novel alleles in the ORSC donors for rice improvement.

Improving rice (Oryza sativa L.) yields is a major objective of breeding programs worldwide. The Oryza rufipogon species complex (ORSC), which includes the rice ancestral species O. rufipogon Griff. and O. nivara S. D. Sharma & Shastry, is an underutilized resource. Using three phenotypically and genotypically diverse ORSC accessions identified as OrA, OrB, and OrC, three Cybonnet x ORSC chromosome segment substitution line (CSSL) libraries were developed to make this genepool more accessible to breeders. The objective was to characterize these libraries for 20 yield-related traits to discover genes not currently deployed for rice improvement. Cybonnet and 212 CSSLs from these libraries were evaluated for 2 years in field studies for six agronomic, six panicle architecture, and eight seed traits. Across the three libraries, 62 CSSLs were found to be significantly different from Cybonnet for one or more traits. Of these, 27 CSSLs were significantly different for seed size traits. To ascertain the chromosome region and underlying candidate gene(s) causing these differences, substitution mapping was performed with previously reported genotypes. Mapping with the CSSLs, which had delayed heading under long days, revealed five known genes associated with rice flowering time pathways. The OsMADS50, RFT1, HD3A, SE1, and GHD7 genes were mapped in the OrB and OrC derived CSSLs but only OsMADS50 mapped in the OrA derived CSSLs. Employing this approach for the other 19 traits revealed 28 total candidate genes. A total of 12 of these genes are currently not deployed for yield enhancement. The introgressed ORSC regions associated with these genes are potential sources of novel variation for rice improvement. Three Cybonnet rice x wild introgression line libraries were evaluated for 20 yield-related traits. Overall, 62 introgression lines were significantly different from Cybonnet for a yield-related trait(s). Substitution mapping narrowed the wild genome region to search for gene(s) affecting yield-related trait(s). Substitution mapping is demonstrated with the five genes affecting days to heading under long day conditions. Of the 28 candidate genes presumed to affect yield traits, 12 are not targeted for breeding, thus potentially novel.

An enduring question in evolutionary biology concerns the degree to which episodes of convergent trait evolution depend on the same genetic programs, particularly over long timescales. In this work, we genetically dissected repeated origins and losses of prickles—sharp epidermal projections—that convergently evolved in numerous plant lineages. Mutations in a cytokinin hormone biosynthetic gene caused at least 16 independent losses of prickles in eggplants and wild relatives in the genus Solanum . Homologs underlie prickle formation across angiosperms that collectively diverged more than 150 million years ago, including rice and roses. By developing new Solanum genetic systems, we leveraged this discovery to eliminate prickles in a wild species and an indigenously foraged berry. Our findings implicate a shared hormone activation genetic program underlying evolutionarily widespread and recurrent instances of plant morphological innovation.

Genetic diversity studies provide an increased understanding of genebank collections and enhance their use for improving global food security. This study explores the genetic variation and population structure of 5738 rice (Oryza sativa L.) accessions representing 39.6% of the O. sativa collection conserved in the AfricaRice genebank of which 74.0% originated from African countries. These accessions were genotyped with 25,904 polymorphic DArTseq-based single nucleotide polymorphisms (SNPs). Genetic distances between pairs of accessions indicate high variability, with 21.0% of pairs being moderately distant and 78.2% highly distant from each other. The genotyped accessions are traditionally grown in six different agro-ecologies from 73 countries. Using neighbor-joining tree, principal component, and model-based population structure analyses, the accessions were divided into four genotypic groups representing the two O. sativa subspecies, Japonica (787 accessions) and Indica, which were further divided into landraces (1879 accessions), and improved cultivars (3027 accessions), and a fourth small group of admixed accessions. Subclusters identifying a specific agro-ecology (upland, lowland, and mangrove swamp) or originating country were noted. Using the maximum length sub-tree method, we selected 10% of the total accessions to form the "AfricaRice O. sativa Core Collection" (AROSCC). The subset of 600 O. sativa accessions captures more than 95% of the SNP polymorphisms in the entire collection. The AROSCC is an important resource to support pre-breeding and rice improvement programs around the world.

CSA NewsVolume 68, Issue 5 p. 42-44 AWARDS Plant Exploration—the ‘Why’ of the Frank N. Meyer Medal Clarice Coyne, Clarice Coyne past chair of the Frank N. Meyer Medal for Plant Genetic Resources CommitteeSearch for more papers by this authorGeorgia C. Eizenga, Georgia C. Eizenga chair of the CSSA Plant Genetic Resources Division (C-8)Search for more papers by this authorMarilyn L. Warburton, Marilyn L. Warburton CSSA past presidentSearch for more papers by this authorShuyu Liu, Shuyu Liu current chair of the Frank N. Meyer Medal for Plant Genetic Resources Committee and past chair of Division C-8Search for more papers by this author Clarice Coyne, Clarice Coyne past chair of the Frank N. Meyer Medal for Plant Genetic Resources CommitteeSearch for more papers by this authorGeorgia C. Eizenga, Georgia C. Eizenga chair of the CSSA Plant Genetic Resources Division (C-8)Search for more papers by this authorMarilyn L. Warburton, Marilyn L. Warburton CSSA past presidentSearch for more papers by this authorShuyu Liu, Shuyu Liu current chair of the Frank N. Meyer Medal for Plant Genetic Resources Committee and past chair of Division C-8Search for more papers by this author First published: 27 April 2023 https://doi.org/10.1002/csan.21020Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL No abstract is available for this article. Volume68, Issue5May 2023Pages 42-44 RelatedInformation

Due to global climate change resulting in extreme temperature fluctuations, it becomes increasingly necessary to explore the natural genetic variation in model crops such as rice to facilitate the breeding of climate-resilient cultivars. To uncover genomic regions in rice involved in managing cold stress tolerance responses and to identify associated cold tolerance genes, two inbred line populations developed from crosses between cold-tolerant and cold-sensitive parents were used for quantitative trait locus (QTL) mapping of two traits: degree of membrane damage after 1 week of cold exposure quantified as percent electrolyte leakage (EL) and percent low-temperature seedling survivability (LTSS) after 1 week of recovery growth. This revealed four EL QTL and 12 LTSS QTL, all overlapping with larger QTL regions previously uncovered by genome-wide association study (GWAS) mapping approaches. Within the QTL regions, 25 cold-tolerant candidate genes were identified based on genomic differences between the cold-tolerant and cold-sensitive parents. Of those genes, 20% coded for receptor-like kinases potentially involved in signal transduction of cold tolerance responses; 16% coded for transcription factors or factors potentially involved in regulating cold tolerance response effector genes; and 64% coded for protein chaperons or enzymes potentially serving as cold tolerance effector proteins. Most of the 25 genes were cold temperature regulated and had deleterious nucleotide variants in the cold-sensitive parent, which might contribute to its cold-sensitive phenotype.

Background Sheath blight (ShB) disease caused by Rhizoctonia solani Kühn, is one of the most economically damaging rice ( Oryza sativa L.) diseases worldwide. There are no known major resistance genes, leaving only partial resistance from small-effect QTL to deploy for cultivar improvement. Many ShB-QTL are associated with plant architectural traits detrimental to yield, including tall plants, late maturity, or open canopy from few or procumbent tillers, which confound detection of physiological resistance. Results To identify QTL for ShB resistance, 417 accessions from the Rice Diversity Panel 1 (RDP1), developed for association mapping studies, were evaluated for ShB resistance, plant height and days to heading in inoculated field plots in Arkansas, USA (AR) and Nanning, China (NC). Inoculated greenhouse-grown plants were used to evaluate ShB using a seedling-stage method to eliminate effects from height or maturity, and tiller (TN) and panicle number (PN) per plant. Potted plants were used to evaluate the RDP1 for TN and PN. Genome-wide association (GWA) mapping with over 3.4 million SNPs identified 21 targeted SNP markers associated with ShB which tagged 18 ShB-QTL not associated with undesirable plant architecture traits. Ten SNPs were associated with ShB among accessions of the Indica subspecies, ten among Japonica subspecies accessions, and one among all RDP1 accessions. Across the 18 ShB QTL, only qShB4-1 was not previously reported in biparental mapping studies and qShB9 was not reported in the GWA ShB studies. All 14 PN QTL overlapped with TN QTL, with 15 total TN QTL identified. Allele effects at the five TN QTL co-located with ShB QTL indicated that increased TN does not inevitably increase disease development; in fact, for four ShB QTL that overlapped TN QTL, the alleles increasing resistance were associated with increased TN and PN, suggesting a desirable coupling of alleles at linked genes. Conclusions Nineteen accessions identified as containing the most SNP alleles associated with ShB resistance for each subpopulation were resistant in both AR and NC field trials. Rice breeders can utilize these accessions and SNPs to develop cultivars with enhanced ShB resistance along with increased TN and PN for improved yield potential.

Crop wild relatives represent valuable reservoirs of variation for breeding, but their populations are threatened in natural habitats, are sparsely represented in genebanks, and most are poorly characterized. The focus of this study is the Oryza rufipogon species complex (ORSC), wild progenitor of Asian rice (Oryza sativa L.). The ORSC comprises perennial, annual and intermediate forms which were historically designated as O. rufipogon, O. nivara, and O. sativa f. spontanea (or Oryza spp., an annual form of mixed O. rufipogon/O. nivara and O. sativa ancestry), respectively, based on non-standardized morphological, geographical, and/or ecologically-based species definitions and boundaries. Here, a collection of 240 diverse ORSC accessions, characterized by genotyping-by-sequencing (113,739 SNPs), was phenotyped for 44 traits associated with plant, panicle, and seed morphology in the screenhouse at the International Rice Research Institute, Philippines. These traits included heritable phenotypes often recorded as characterization data by genebanks. Over 100 of these ORSC accessions were also phenotyped in the greenhouse for 18 traits in Stuttgart, Arkansas, and 16 traits in Ithaca, New York, United States. We implemented a Bayesian Gaussian mixture model to infer accession groups from a subset of these phenotypic data and ascertained three phenotype-based group assignments. We used concordance between the genotypic subpopulations and these phenotype-based groups to identify a suite of phenotypic traits that could reliably differentiate the ORSC populations, whether measured in tropical or temperate regions. The traits provide insight into plant morphology, life history (perenniality versus annuality) and mating habit (self- versus cross-pollinated), and are largely consistent with genebank species designations. One phenotypic group contains predominantly O. rufipogon accessions characterized as perennial and largely out-crossing and one contains predominantly O. nivara accessions characterized as annual and largely inbreeding. From these groups, 42 “core” O. rufipogon and 25 “core” O. nivara accessions were identified for domestication studies. The third group, comprising 20% of our collection, has the most accessions identified as Oryza spp. (51.2%) and levels of O. sativa admixture accounting for more than 50% of the genome. This third group is potentially useful as a “pre-breeding” pool for breeders attempting to incorporate novel variation into elite breeding lines.

Oryza nivara is considered one of the wild progenitors of cultivated Asian rice (O. sativa). An O. nivara (IRGC104443) accession, previously identified as being moderately resistant to rice sheath blight disease, was used as the donor parent to develop an advanced backcross population with the U.S. rice (O. sativa) cultivar, LaGrue, as the recurrent parent. The population was genotyped with 210 DNA markers and a linkage map constructed that spanned 1488.9 cM. Sheath blight (ShB) disease was evaluated in both greenhouse and field conditions. Days to heading (DTHD), plant height (PTHT) and culm (angle) habit (CULMHAB) were recorded because they can confound sheath blight disease ratings under field conditions. Multiple interval mapping identified qShB9 as the ShB-QTL being the source of resistance and the resistance was attributed to the O. nivara allele. The single CULMHAB QTL, qCULMHAB9, was also located in this region but had a different peak suggesting the more open tillering was most likely due to the TILLER ANGLE CONTROL-1 gene which was fine-mapped near the chromosome 9 ShB resistance in other O. sativa populations. The ShB QTL, qShB3-2-mc, identified in the greenhouse study was not verified in the field studies. None of the three DTHD QTL were colocalized with ShB QTL, while the single PTHT QTL was mapped to the region of the semi-dwarf-1 gene for short stature on chromosome 1. Further studies will be undertaken to fine map the qShB9 region and identify linked markers for use in cultivar development.

Abstract There is a large gap between genomewide association studies (GWAS) and developing markers that can be used in marker‐assisted selection (MAS) schemes for cultivar improvement. This study is a prototype for developing markers using segregating single nucleotide polymorphisms (SNPs) for panicle architecture and grain shape traits identified by GWAS in the Rice Diversity Panel‐1 and colocalized in QTL regions revealed by linkage mapping in the Estrela × NSFTV199 rice (Oryza sativa L.) population. Markers were developed from sequence variants suitable for reliable detection in regions surrounding the most significant SNPs identified in GWAS. Once developed, the markers were validated in three Japonica subspecies biparental populations, used to improve QTL mapping resolution, and employed to select potential parents for use in MAS. All marker alleles segregated in the rice tropical japonica subpopulation.

[This corrects the article DOI: 10.3389/fpls.2020.564824.].

Two rice (Oryza sativa L.) germplasm lines, SC14_166 (Reg. no. GP-148, PI 698103) and SC14_072 (Reg. no. GP-147, PI 698102), containing alleles for increased panicle branching, seeds per panicle, and grain length were developed by the USDA-ARS. They are recombinant inbred lines selected from a cross of 'Estrela' (GSOR 301227) and NSFTV199 (GSOR 301190), both of tropical japonica origin. SC14_166 is a medium grain cultivar and contains alleles for two major genes, SPIKELET NUMBER on chromosome (chr.) 4 and FRIZZY PANICLE on chr. 7, which result in a greater number of primary branches, seeds per panicle, and panicle weight compared with the parents. SC14_072 is an extra-long grain cultivar and contains alleles for two major genes on chr. 3, GRAIN SIZE 3 and GRAIN LENGTH 3.2, resulting in greater grain length, width, thickness, and kernel weight. The germplasm lines possess Pi-ks, whereas SC_072 also has Pi-z, both of which are major genes for resistance to rice blast disease. These germplasm lines are well adapted to growing conditions in the southern United States and will benefit long-grain and medium-grain breeding programs that desire to increase grain dimensions and panicle architecture traits. Because they are derived from the tropical japonica subpopulation like most U.S. cultivars, they will be highly compatible for making breeding crosses and will contribute novel alleles to the gene pool.

Rice, Oryza sativa L., is a cultivated, inbreeding species that serves as the staple food for the largest number of people on earth. It has two strongly diverged varietal groups, Indica and Japonica , which result from a combination of natural and human selection. The genetic divergence of these groups reflects the underlying population structure of their wild ancestors, and suggests that a pre-breeding strategy designed to take advantage of existing genetic, geographic and ecological substructure may provide a rational approach to the utilization of crop wild ancestors in plant improvement. Here we describe the coordinated development of six introgression libraries ( n = 63 to 81 lines per library) in both Indica (cv. IR64) and Japonica (cv. Cybonnet) backgrounds using three bio-geographically diverse wild donors representing the Oryza rufipogon Species Complex from China, Laos and Indonesia. The final libraries were genotyped using an Infinium 7K rice SNP array (C7AIR) and analyzed under greenhouse conditions for several simply inherited (Mendelian) traits. These six interspecific populations can be used as individual Chromosome Segment Substitution Line libraries and, when considered together, serve as a powerful genetic resource for systematic genetic dissection of agronomic, physiological and developmental traits in rice.

Manganese (Mn) is an essential trace element for plants and commonly contributes to human health; however, the understanding of the genes controlling natural variation in Mn in crop plants is limited. Here, the integration of two of genome-wide association study approaches was used to increase the identification of valuable quantitative trait loci (QTL) and candidate genes responsible for the concentration of grain Mn across 389 diverse rice cultivars grown in Arkansas and Texas, USA, in multiple years. Single-trait analysis was initially performed using three different SNP datasets. As a result, significant loci could be detected using the high-density SNP dataset. Based on the 5.2 M SNP dataset, major QTLs were located on chromosomes 3 and 7 for Mn containing six candidate genes. In addition, the phenotypic data of grain Mn concentration were combined from three flooded-field experiments from the two sites and 3 years using multi-experiment analysis based on the 5.2 M SNP dataset. Two previous QTLs on chromosome 3 were identified across experiments, whereas new Mn QTLs were identified that were not found in individual experiments, on chromosomes 3, 4, 9 and 11. OsMTP8.1 was identified in both approaches and is a good candidate gene that could be controlling grain Mn concentration. This work demonstrates the utilisation of multi-experiment analysis to identify constitutive QTLs and candidate genes associated with the grain Mn concentration. Hence, the approach should be advantageous to facilitate genomic breeding programmes in rice and other crops considering QTLs and genes associated with complex traits in natural populations.

Genebanks conserve worldwide crop genetic diversity in systematically assembled and maintained ex situ collections for use by plant breeders and geneticists to improve the productivity, value, and sustainability of agriculture. Challenges faced in genebank management include providing sufficient and accurate trait information to facilitate searching the collection; controlling redundant accessions, seed mixtures, and mislabeled accessions; and identifying gaps in diversity. To help address these issues, a system that employs genotyping using 24 trait-specific markers (TSMs), fingerprint markers (FPMs), or markers that are unique to subspecies was implemented for the USDA-ARS National Plant Germplasm System (NPGS), National Small Grains Collection (NSGC) for rice (Oryza sativa L.). Trait-specific markers were used to validate phenotypic data for fragrance, pericarp color, apparent amylose content, starch pasting properties, gelatinization temperature, resistance to rice blast disease, plant pubescence, and plant height. Discrepancies between genotypic and phenotypic data are useful for quality control during curation or may present opportunities for identifying novel alleles, particularly for TSMs. Over 2,000 accessions were classified by species, O. sativa or O. glaberrima Steud.; subspecies, Indica or Japonica; and subpopulation, aromatic, indica, aus, temperate japonica, or tropical japonica using the subspecies marker and FPMs. This small panel of TSMs and FPMs was also adequate for differentiating important U.S. cultivars, which are primarily of tropical japonica background. As a result of this study, TSM and FPM descriptors will be added to the rice NSGC database, redundancies reduced, and mislabeled accessions corrected, thus increasing the value of the rice NSGC for breeding programs and providing new opportunities for gene discovery.

The Rice Diversity Panel 1 (RDP1) was developed for genome-wide association (GWA) studies to explore five rice ( L.) subpopulations (, , , , and ). The RDP1 was evaluated for over 30 traits, including agronomic, panicle architecture, seed, and disease traits and genotyped with 700,000 single nucleotide polymorphisms (SNPs). Most rice grown in the southern United States is and thus the diversity in this subpopulation is interesting to U.S. breeders. Among the RDP1 accessions, 'Estrela' and 'NSFTV199' are both phenotypically and genotypically diverse, thus making them excellent parents for a biparental mapping population. The objectives were to (i) ascertain the GWA QTLs from the RDP1 GWA studies that overlapped with the QTLs uncovered in an Estrela × NSFTV199 recombinant inbred line (RIL) population evaluated for 15 yield traits, and (ii) identify known or novel genes potentially controlling specific yield component traits. The 256 RILs were genotyped with 132 simple sequence repeat markers and 70 QTLs were found. Perl scripts were developed for automatic identification of the underlying candidate genes in the GWA QTL regions. Approximately 100 GWA QTLs overlapped with 41 Estrela × NSFTV199 QTL (RIL QTL) regions and 47 known genes were identified. Two seed trait RIL QTLs with overlapping GWA QTLs were not associated with a known gene. Segregating SNPs in the overlapping GWA QTLs for RIL QTLs with high values will be evaluated as potential DNA markers useful to breeding programs for the associated yield trait.

Understanding the genetic variation for yield‐related traits in tropical japonica rice (Oryza sativa L.) is extremely important to US rice breeding because most US rice is from this subpopulation. The Estrela × NSFTV199 mapping population (Reg. no. MP‐8, NSL 530337 MAP) was developed from the Rice Diversity Panel 1 accessions Estrela (GSOR 301227), an admixture of japonica, and NSFTV199 (GSOR 301190), a tropical japonica. Both accessions were characterized as phenotypically and genotypically diverse from each other. The population consists of 276 F2:9 recombinant inbred lines (RILs) and parents (GSOR 104001 through GSOR 104282), which were genotyped with 65 simple sequence repeat (SSR) markers and 256 RILs genotyped with an additional 69 SSR markers. The population was phenotyped for eight agronomic traits (days to heading, plant height, flag leaf length and width, leaf pubescence, culm habit, awn presence, and seed shattering), six panicle architecture traits (panicle length; number of primary branches, florets, seeds, and sterile florets per panicle; and percentage fertility), and nine grain traits (seed length, width, and length‐to‐width ratio with and without the hull; percentage chalk in brown rice with and without the broken kernels, and 100‐seed weight). Here within we report the evaluation of the population for eight of the traits. Quantitative trait loci associated with 22 of these 23 traits were identified. This population represents a valuable resource for basic genomic studies and applied marker‐assisted breeding efforts.

Acquisition and rearrangement of host genes by transposable elements (TEs) is an important mechanism to increase gene diversity as exemplified by the ∼3000 Pack-Mutator-like TEs in the rice genome which have acquired gene sequences (Pack-MULEs), yet remain enigmatic. To identify signatures of functioning Pack-MULEs and Pack-MULE evolution, we generated transcriptome, translatome, and epigenome datasets and compared Pack-MULEs to genes and other TE families. Approximately 40% of Pack-MULEs were transcribed with 9% having translation evidence, clearly distinguishing them from other TEs. Pack-MULEs exhibited a unique expression profile associated with specificity in reproductive tissues that may be associated with seed traits. Expressed Pack-MULEs resemble regular protein-coding genes as exhibited by a low level of DNA methylation, association with active histone marks and DNase I hypersensitive sites, and an absence of repressive histone marks, suggesting that a substantial fraction of Pack-MULEs are potentially functional in vivo. Interestingly, the expression capacity of Pack-MULEs is independent of the local genomic environment, and the insertion and expression of Pack-MULEs may have altered the local chromosomal expression pattern as well as counteracted the impact of recombination on chromosomal base composition, which has profound consequences on the evolution of chromosome structure.