Genetic bases of source-,sink-,and yield-related traits revealed by genome-wide association study in Xian rice

The source-sink relationship determines the ultimate grain yield.We investigated the genetic basis of the relationship between source and sink and yield potential in rice.In two environments,we identified quantitative trait loci(QTL)associated with sink capacity(total spikelet number per panicle and thousand-grain weight),source leaf(flag leaf length,flag leaf width and flag leaf area),source-sink relationship(total spikelet number to flag leaf area ratio)and yield-related traits(filled grain number per panicle,panicle number per plant,grain yield per plant,biomass per plant,and harvest index)by genome-wide association analysis using 272 Xian(indica)accessions.The panel showed substantial variation for all traits in the two environments and revealed complex phenotypic correlations.A total of 70 QTL influencing the 11 traits were identified using 469,377 high-quality SNP markers.Five QTL were detected consistently in four chromosomal regions in both environments.Five QTL clusters simultaneously affected source,sink,source–sink relationship,and grain yield traits,probably explaining the genetic basis of significant correlations of grain yield with source and sink traits.We selected 24 candidate genes in the four consistent QTL regions by identifying linkage disequilibrium(LD)blocks associated with significant SNPs and performing haplotype analysis.The genes included one cloned gene(NOG1)and three newly identified QTL(qHI6,qTGW7,and qFLA8).These results provide a theoretical basis for high-yield rice breeding by increasing and balancing source–sink relationships using marker-assisted selection.

Genetic background effects on QTL and QTL × environment interaction for yield and its component traits as revealed by reciprocal introgression lines in rice

QTLs for quantitative traits are influenced by genetic background(GB) and environment.Identification of QTL with GB independency and environmental stability is prerequisite for effective marker-assisted selection(MAS). In this study, QTLs and QTL × environment interactions affecting grain yield per plant(GY) and its component traits, filled grain number per panicle(FGN), panicle number per plant(PN) and 1000-grain weight(TGW) across six environments were dissected using two sets of reciprocal introgression lines(ILs) derived from the cross Lemont × Teqing and SNP genotypic data. ANOVA indicated that the differences among genotypes and environments within each set of ILs were highly significant for all traits. A total of 72 distinct QTLs for GY and its component traits including 15 for GY, 25 for FGN, 18 for PN, and 29 for TGW were detected over the six environments. Most QTLs(87.4%) showed significant QTL × environment interactions(QEIs) and appeared to be more or less environment-specific. Among 72 QTLs, 15(20.8%) QTLs and 12(16.7%) QEIs were commonly identified in both backgrounds, indicating QTL especially QEI for yield and its component traits had strong GB effects. Four QTL regions affecting GY and its component traits, including S1269707–S4288071, S16661497–S17511092, and S35861863–S36341768 on chromosome 3, and S4134205–S7643153 on chromosome 5, were detected in both backgrounds and coincided with cloned genes for yield-related traits. These regions can be the targeted in rice breeding for high yield potential through MAS. Application of QTL main effects and their environmental interaction effects in MAS was discussed in detail.

Comparison of the photo-acclimation potential of fl oating and benthic thalli of Sargassum horneri(Phaeophyta)during autumn and winter

Sargassum horneri is a foundational species and an important contributor to the fl oating seaweed stock along the northeastern coast of Asia.In this study,benthic and fl oating thalli of S.horneri were collected from Changdao Island(37°54′N,120°43′E),Bohai Bay,China.We conducted an in-situ and an indoor experiment to study the acclimation potential in S.horneri to abiotic conditions at sea surface in autumn and winter.Both benthic and fl oating thalli were cultured in situ for two months(from October to December)at diff erent depths:0 m above sea level(masl)and 3 m below sea level(mbsl),and their growth rate,biochemical content,and photosynthetic performance were compared.During the fi rst month of culture,the relative growth rate of fl oating thalli was 2-fold greater than that of benthic thalli at 0 masl.The photosynthetic rate of most thalli was signifi cantly higher at 0 masl than at 3 mbsl.In the indoor experiments,fl oating and benthic thalli were exposed to high light intensity(400μmol photons/(m^(2)·s)photosynthetically active radiation(PAR))for 21 d,and their photo-acclimation capacities were compared.Under high light intensity,the two types of thalli showed low maximum quantum yield(F_(v)/F_(m))and light utilisation effi ciency(α)but high light saturation point(E_(k)).Floating thalli showed higher photosynthetic rate and photoprotective ability than benthic thalli at high light intensity.The eff ective quantum yield of photosystem II[Y(II)]of both types of thalli recovered after a 6-day treatment with low light intensity(40μmol photons/(m^(2)·s)).These fi ndings suggest that S.horneri is highly acclimated to the sea surface environment,which possibly contributes to its rapid accumulation and long free-fl oating periods at the sea surface.

Developing green super rice varieties with high nutrient use efficiency by phenotypic selection under varied nutrient conditions

The development of green super rice varieties with improved nutrient use efficiency(NuUE)is a vital target area to increase yield and make it more stable under rainfed conditions.In the present study, we followed an early backcross(BC) breeding approach by using a highyielding and widely adapted Xian variety, Weed Tolerant Rice 1(WTR-1), as a recipient and a Geng variety, Hao-An-Nong(HAN), as a donor.Starting from the BC1F2 generation, the BC population went through one generation of selection under irrigated, low-input, and rainfed conditions, followed by four consecutive generations of screening and selection for high grain yield(GY) under six different nutrient conditions(NPK, 75 N,-N,-P,-NP, and-NPK), leading to the development of 230 BC1F6 introgression lines(ILs).These 230 ILs were evaluated under the same six nutrient conditions for 13 agro-morphological and grain yield component traits in comparison to four checks and parents.Significant trait variations were observed between the treatments and ILs.Positive correlations were identified for GY with biomass, panicle length, flag-leaf area, flag-leaf width, filled grain number per panicle,1000-grain weight, and tiller number under-N,-P,-NP, and-NPK conditions.Out of 230 ILs,12 were identified as promising under two or more nutrient deficiency conditions.The results demonstrated an efficient inter-subspecific BC breeding procedure with a first round of selection under rainfed-drought conditions, followed by four generations of progeny testing for yield performance under six nutrient conditions.The promising ILs can be useful resources for molecular genetic dissection and understanding the physiological mechanisms of NuUE.

Allelic impacts on pre-harvest sprouting resistance and favorable haplotypes in Ta PHS1 of Chinese wheat accessions

Pre-harvest sprouting(PHS)influences yield and end-use quality of bread wheat.Developing varieties with PHS resistance is the most effective way to reduce this problem.In this study,a panel of 725 Chinese wheat accessions were evaluated for PHS resistance in three environments.There was abundant variation in PHS resistance and 63 accessions showing high resistance had germination rates of less than 10%across three experiments.The distribution of three causal single nucleotide polymorphisms in Ta PHS1 at bases-222,+646,and+666 were assessed and frequencies were determined.Favorable alleles conferring PHS resistance were identified for each locus.Haplotype analysis showed that bases C,G,and A at each of the three loci comprised the best haplotype for PHS resistance,whereas TAT showed the highest sprouting rate.Accessions with the superior Ta PHS1 haplotypes proved to be resistant to PHS providing a basis to develop varieties with PHS resistance through marker assisted breeding.

High-Resolution Genome-wide Association Study Identifies Genomic Regions and Candidate Genes for Important Agronomic Traits in Wheat

Wheat(Triticum aestivum)is a major staple food crop worldwide.Genetic dissection of important agronomic traits is essential for continuous improvement of wheat yield to meet the demand of the world's growing population.We conducted a large-scale genome-wide association study(GWAS)using a panel of 768 wheat cultivars that were genotyped with 327609 single-nucleotide polymorphisms generated by genotyping-by-sequencing and detected 395 quantitative trait loci(QTLs)for 12 traits under 7 environments.Among them,273 QTLs were delimited to≤1.0-Mb intervals and 7 of them are either known genes(Rht-D,Vrn-B1,and Vrn-D1)that have been cloned or known QTLs(TaGA2ox8,APO1,TaSus1-7B,and Rht12)that were previously mapped.Eight putative candidate genes were identified for three QTLs that enhance spike seed setting and grain size using gene expression data and were validated in three bi-parental populations.Protein sequence analysis identified 33 putative wheat orthologs that have high identity with rice genes in QTLs affecting similar traits.Large r^2 values for additive effects observed among the QTLs for most traits indicated that the phenotypes of these identified QTLs were highly predictable.Results from this study demonstrated that significantly increasing GWAS population size and marker density greatly improves detection and identification of candidate genes underlying a QTL,solidifying the foundation for large-scale QTL fine mapping,candidate gene validation,and developing functional markers for genomics-based breeding in wheat.