Genetic Variation and Association Analysis of the SSR Markers Linked to the Major Drought-Yield QTLs of Rice

Association study of morpho-phenological traits in quinoa (Chenopodium quinoa Willd.) using SSR markers

In this study, the genetic and molecular diversity of 60 quinoa accessions was assessed using agronomically important traits related to grain yield as well as microsatellite (SSR) markers, and informative markers linked to the studied traits were identified using association study. The results showed that most of the studied traits had a relatively high diversity, but grain saponin and protein content showed the highest diversity. High diversity was also observed in all SSR markers, but KAAT023, KAAT027, KAAT036, and KCAA014 showed the highest values for most of the diversity indices and can be introduced as the informative markers to assess genetic diversity in quinoa. Population structure analysis showed that the studied population probably includes two subclusters, so that out of 60 quinoa accessions, 29 (48%) and 23 (38%) accessions were assigned to the first and second subclusters, respectively, and eight (13%) accessions were considered as the mixed genotypes. The study of the population structure using Structure software showed two possible subgroups (K = 2) in the studied population and the results of the bar plot confirmed it. Association study using the general linear model (GLM) and mixed linear model (MLM) identified the number of 35 and 32 significant marker-trait associations (MTAs) for the first year (2019) and 37 and 35 significant MTAs for the second year (2020), respectively. Among the significant MTAs identified for different traits, the highest number of significant MTAs were obtained for grain yield and 1000-grain weight with six and five MTAs, respectively.

Enhancing stress resilience in rice (Oryza sativa L.) through profiling early-stage morpho-physiological and molecular responses to multiple abiotic stress tolerance

Under changing climatic conditions, crop plants are more adversely affected by a combination of various abiotic stresses than by a single abiotic stress. Therefore, it is essential to identify potential donors to multiple abiotic stresses for developing climate-resilient crop varieties. Hence, the present study was undertaken with 41 germplasm accessions comprising native landraces of Tamil Nadu, Prerelease lines and cultivars were screened independently for drought, salinity, and submergence at the seedling stage during Kharif and Rabi 2022-2023. Stress was imposed separately for these three abiotic stresses on 21-day-old seedlings and was maintained for 10 days. The studied genotypes showed a significant reduction in plant biomass (PB), Relative Growth Index (RGI), relative water content (RWC), leaf photosynthesis, chlorophyll fluorescence, and Chlorophyll Concentration Index (CCI) under drought followed by salinity and submergence. Stress-tolerant indices for drought, salinity, and submergence revealed significant variation for plant biomass. Furthermore, a set of 30 SSR markers linked to drought, salinity, and submergence QTLs has been used to characterize 41 rice germplasm accessions. Our analysis suggests a significantly high polymorphism, with 28 polymorphic markers having a 93.40% in 76 loci. The mean values of polymorphic information content (PIC), heterozygosity index (HI), marker index (MI), and resolving power (RP) were 0.369, 0.433, 1.140, and 2.877, respectively. Jaccard clustering grouped all the genotypes into two major and six subclusters. According to STRUCTURE analysis, all genotypes were grouped into two major clusters, which are concurrent with a very broad genetic base (K = 2). Statistically significant marker-trait associations for biomass were observed for five polymorphic markers, viz., RM211, RM212 (drought), RM10694 (salinity), RM219, and RM21 (submergence). Similarly, significant markers for relative shoot length were observed for RM551 (drought), RM10694 (salinity), and ART5 (submergence). Notably, the genotypes Mattaikar, Varigarudan samba, Arupatham samba, and APD19002 were identified as potential donors for multiple abiotic stress tolerance. Thus, identifying the genetic potential of germplasm could be useful for enhancing stress resilience in rice.

De novo assembly of Iron-Heart Cunninghamia lanceolata transcriptome and EST-SSR marker development for genetic diversity analysis

Iron-Heart Cunninghamia lanceolata, a wild relative of Chinese fir with valuable genetic and breeding traits, has been limited in genetic studies due to a lack of genomic resources and markers. In this study, we conducted transcriptome sequencing of Iron-Heart C. lanceolata leaves using Illumina NovaSeq 6000 and performed assembly and analysis. We obtained 45,326,576 clean reads and 115,501 unigenes. Comparative analysis in five functional databases resulted in successful annotation of 26,278 unigenes, with 6,693 unigenes annotated in all databases (5.79% of the total). UniProt and Pfam databases provided annotations for 22,673 and 18,315 unigenes, respectively. Gene Ontology analysis categorized 23,962 unigenes into three categories. KEGG database alignment annotated 10,195 unigenes, classifying them into five categories: metabolism, genetic information, biological systems, cellular processes, and environmental information processing. From the unigenes, we identified 5,645 SSRs, with dinucleotides repeats being the most common (41.47%). We observed variations in repeat numbers and base compositions, with the majority of markers ranging from 12 to 29 bp in length. We randomly selected 200 primer pairs and successfully amplified 15 pairs of polymorphic SSR primers, which effectively distinguished Chinese fir plants of different origins. This study provides insights into the genetic characteristics of Iron-Heart C. lanceolata and offers a foundation for future molecular marker development, breeding programs, genetic diversity analysis, and conservation strategies.

Mapping QTLs for yield and photosynthesis-related traits in three consecutive backcross populations of Oryza sativa cultivar Cottondora Sannalu (MTU1010) and Oryza rufipogon

Identification of trait enhancing QTLs for yield and photosynthesis-related traits in rice using interspecific mapping population and chromosome segment substitution lines derived from a cross between Oryza sativa and Oryza rufipogon. Wild rice contains novel genes which can help in improving rice yield. Common wild rice Oryza rufipogon is a known source for enhanced photosynthesis and yield-related traits. We developed BC₂F_2:3:4 mapping populations using O. rufipogon IC309814 with high photosynthetic rate as donor, and elite cultivar MTU1010 as recurrent parent. Evaluation of 238 BC₂F₂ families for 13 yield-related traits and 208 BC₂F₂ families for seven photosynthesis-related physiological traits resulted in identification of significantly different lines which performed better than MTU1010 for various yield contributing traits. 49 QTLs were identified for 13 yield traits and 7 QTLs for photosynthesis-related traits in BC₂F_2. In addition, 34 QTLs in BC₂F₃ and 26 QTLs in BC₂F₄ were also detected for yield traits.11 common QTLs were identified in three consecutive generations and their trait-increasing alleles were derived from O. rufipogon. Significantly, one major effect common QTL qTGW3.1 for thousand grain weight with average phenotypic variance 8.1% and one novel QTL qBM7.1 for biomass were identified. Photosynthesis-related QTLs qP_N9.1, qP_N12.1, qP_N12.2 qSPAD1.1 and qSPAD6.1 showed additive effect from O. rufipogon. A set of 145 CSSLs were identified in BC₂F₂ which together represented 87% of O. rufipogon genome. In addition, 87 of the 145 CSSLs were significantly different than MTU1010 for at least one trait. The major effect QTLs can be fine mapped for gene discovery. CSSLs developed in this study are a good source of novel alleles from O. rufipogon in the background of Cottondora Sannalu for rapid improvement of any trait in rice.

Draft Sequencing Crested Wheatgrass Chromosomes Identified Evolutionary Structural Changes and Genes and Facilitated the Development of SSR Markers

Crested wheatgrass (Agropyron cristatum), a wild relative of wheat, is an attractive source of genes and alleles for their improvement. Its wider use is hampered by limited knowledge of its complex genome. In this work, individual chromosomes were purified by flow sorting, and DNA shotgun sequencing was performed. The annotation of chromosome-specific sequences characterized the DNA-repeat content and led to the identification of genic sequences. Among them, genic sequences homologous to genes conferring plant disease resistance and involved in plant tolerance to biotic and abiotic stress were identified. Genes belonging to the important groups for breeders involved in different functional categories were found. The analysis of the DNA-repeat content identified a new LTR element, Agrocen, which is enriched in centromeric regions. The colocalization of the element with the centromeric histone H3 variant CENH3 suggested its functional role in the grass centromere. Finally, 159 polymorphic simple-sequence-repeat (SSR) markers were identified, with 72 of them being chromosome- or chromosome-arm-specific, 16 mapping to more than one chromosome, and 71 mapping to all the Agropyron chromosomes. The markers were used to characterize orthologous relationships between A. cristatum and common wheat that will facilitate the introgression breeding of wheat using A. cristatum.

Molecular Genetic Diversity and Combining Ability for Some Physiological and Agronomic Traits in Rice under Well-Watered and Water-Deficit Conditions

Water deficit is a pivotal abiotic stress that detrimentally constrains rice growth and production. Thereupon, the development of high-yielding and drought-tolerant rice genotypes is imperative in order to sustain rice production and ensure global food security. The present study aimed to evaluate diverse exotic and local parental rice genotypes and their corresponding cross combinations under water-deficit versus well-watered conditions, determining general and specific combining ability effects, heterosis, and the gene action controlling important traits through half-diallel analysis. In addition, the research aimed to assess parental genetic distance (GD) employing simple sequence repeat (SSR) markers, and to determine its association with hybrid performance, heterosis, and specific combining ability (SCA) effects. Six diverse rice genotypes (exotic and local) and their 15 F1 hybrids were assessed for two years under water-deficit and well-watered conditions. The results revealed that water-deficit stress substantially declined days to heading, plant height, chlorophyll content, relative water content, grain yield, and yield attributes. Contrarily, leaf rolling and the sterility percentage were considerably increased compared to well-watered conditions. Genotypes differed significantly for all the studied characteristics under water-deficit and well-watered conditions. Both additive and non-additive gene actions were involved in governing the inheritance of all the studied traits; however, additive gene action was predominant for most traits. The parental genotypes P1 and P2 were identified as excellent combiners for earliness and the breeding of short stature genotypes. Moreover, P3, P4, and P6 were identified as excellent combiners to increase grain yield and its attributes under water-deficit conditions. The hybrid combinations; P1 × P4, P2 × P5, P3 × P4, and P4 × P6 were found to be good specific combiners for grain yield and its contributed traits under water-deficit conditions. The parental genetic distance (GD) ranged from 0.38 to 0.89, with an average of 0.70. It showed lower association with hybrid performance, heterosis, and combining ability effects for all the studied traits. Nevertheless, SCA revealed a significant association with hybrid performance and heterosis, which suggests that SCA is a good predictor for hybrid performance and heterosis under water-deficit conditions. Strong positive relationships were identified between grain yield and each of relative water content, chlorophyll content, number of panicles/plant, number of filled grains/panicle, and 1000-grain weight. This suggests that these traits could be exploited as important indirect selection criteria for improving rice grain yield under water-deficit conditions.

Genome survey sequencing and characterization of simple sequence repeat (SSR) markers in Platostoma palustre (Blume) A.J.Paton (Chinese mesona)

Platostoma palustre (Blume) A.J.Paton is an annual herbaceous persistent plant of the Labiatae family. However, there is a lack of genomic data for this plant, which severely restricts its genetic improvement. In this study, we performed genome survey sequencing of P. palustre and developed simple sequence repeat (SSR) markers based on the resulting sequence. K-mer analysis revealed that the assembled genome size was approximately 1.21 Gb. A total of 15,498 SSR motifs were identified and characterized in this study; among them, dinucleotide, and hexanucleotide repeats had the highest and lowest, respectively. Among the dinucleotide repeat motifs, AT/TA repeat motifs were the most abundant, and GC/CG repeat motifs were rather rare, accounting for 44.28% and 0.63%, respectively. Genetic similarity coefficient analysis by the UPMGA methods clustered 12 clones, of P. palustre and related species into two subgroups. These results provide helpful information for further research on P. palustre resources and variety improvements.

Genetic Diversity of Shanlan Upland Rice (Oryza sativa L.) and Association Analysis of SSR Markers Linked to Agronomic Traits

Shanlan upland rice, a kind of unique rice germplasm in Hainan Island, was used to evaluate genetic diversity and association between SSR markers and agronomic traits. A total of 239 alleles were detected in 57 Hainan upland rice varieties using 35 SSR markers, and the number of alleles per locus was 2-19. The observed heterozygosity was 0.0655-0.3115. The Shannon diversity index was 0.1352-0.4827. The genetic similarity coefficient was 0.6736-0.9707, and 46 varieties were clustered into one group, indicating that the genetic base of the Shanlan upland rice germplasm was narrow. A total of 25 SSR markers significantly related to plant height, effective panicle number per plant, panicle length, total grain number, filled grain number, seed rating rate, and 1000-grain weight were obtained (P < 0.01), with the percentage of the total variations explained ranging from 0.12% to 42.62%. RM208 explained 42.62% of the total variations in plant height of Shanlan upland rice. RM493 was significantly associated with 6 agronomic traits. We can speculate that RM208 may flank QTLs responsible for plant height and RM493 may flank QTLs playing a fundamental role in the intertwined regulatory network of agronomic traits of Shanlan upland rice.

Utilization of genetic diversity and marker-trait to improve drought tolerance in rice (Oryza sativa L.)

Drought stress is one of the main problems for the rice crop, as it reduces the production and productivity of the grain yield significantly. In Egypt, many restrictions were made on the cultivation of rice due to its high-water demand. Producing promising drought-tolerant rice cultivars combined with high yielding is one of the main targets for rice breeders. A set of 22 highly diverse rice genotypes were evaluated under normal and drought conditions. Morphological, physiological, and yield traits were recorded on each genotype. Drought susceptibility index (DSI) was estimated for six yield traits to identify the most drought-tolerant rice genotypes. A high genetic variation was found among genotypes tested in the experiment. Under normal conditions, the highest phenotypic correlation was found between grain yield (GY) and sterility percentage (SP) (- 0.73**), while it was among GY and chlorophyll content (CC) (0.82**) under drought conditions. To identify quantitative trait loci (QTL) controlling yielding traits under drought and normal, a single marker analysis was performed between all yield traits under both conditions and a set of 106 simple sequence repeat (SSR) marker alleles. The genetic association analysis revealed 14 and 17 QTL under drought and normal conditions, respectively. The most drought-tolerant genotypes were selected based on phenotypic traits, the number of QTL in each selected genotype, and the level of genetic diversity existed among the genotypes. As a result, five genotypes (Giza 178, IET1444, GZ1368-S-5-4, Nahda, Giza 14) were identified as the most promising drought-tolerant rice genotypes. Eight QTL controlling drought tolerance were identified in Giza 178, Nahda, and GZ1368-S-5-4, while four QTL were found in IET1444. The number of different QTLs were estimated among the five selected genotypes. Giza 178 and GZ1368-S-5-4 shared the same QTLs. Seven different QTLs were found among Nahda, IET1444, GZ1368-S-5-4, and Giza 14. Combining information from phenotypic traits, genetic diversity analysis, and QTL analysis was very useful in identifying the true drought-tolerant rice genotypes that can be used for crossing in the future breeding program.

Population Genetics of Calotropis gigantea, a Medicinal and Fiber Resource Plant, as Inferred from Microsatellite Marker Variation in two Native Countries

Calotropis gigantea is well known for its aesthetic, medicinal, pharmacological, fodder, fuel, and fiber production potential. Unfortunately, this plant species is still undomesticated, and the genetic information available for crop improvement is limited. For this study, we sampled 21 natural populations of C. gigantea from two key areas of its natural distribution range (Bangladesh and China) and genotyped 379 individuals using nine nuclear microsatellite markers. Population genetic diversity was higher in Bangladesh than that observed in Chinese populations. Overall, a moderate level of genetic diversity was found (N_a = 3.73, H_E = 0.466), with most of the genetic variation detected within populations (65.49%) and substantial genetic differentiation (F_ST = 0.345) between the study regions. We observed a significant correlation between genetic and geographic distances (r  =  0.287, P  =  0.001). The Bayesian clustering, UPGMA tree, and PCoA analyses yielded three distinct genetic pools, but the number of migrants per generation was high (N_M = 0.52-2.78) among them. Our analyses also revealed that some populations may have experienced recent demographic bottlenecks. Our study provides a baseline for exploitation of the genetic resources of C. gigantea in domestication and breeding programs as well as some insights into the germplasm conservation of this valuable plant.