Probable omnigenic effect and evolutionary insights of aerobic adaptation allele OsNCED2T on qDTY12.1 effecting grain yield under reproductive stage drought stress in rice

Yield associated quantitative trait loci (qDTY) under drought stress provides significant advantage for grain yield in rice. The major, stable qDTY12.1 was identified in a mapping population developed from upland cultivars Vandana and Way Rarem. Further, introgression line comprising of qDTY12.1 genomic region was characterized to have multiple genes (NAM, DECUSSATE) regulating the drought tolerance under severe drought stress substantiated through recently proposed omnigenic model for complex traits. Recently, plastid localized NCED2T allele present within the qDTY12.1 genomic region was characterized for conferring aerobic adaptation in lowland varieties. Since, NCED2T is evolutionary fixed in upland cultivars and Vandana was found to have the favorable allele of NCED2T, we hypothesized that this favorable allele might confer omnigenic effect on qDTY12.1 genes. Our evolutionary analysis using non synonymous SNPs present in genes namely NCED, NAM, and DECUSSATE and qDTY12.1 genomic regions showed specific grouping of Vandana with upland cultivars only for NCED gene and its adjoining genomic regions. However, non synonymous SNPs in NAM and DECUSSATE genes and its adjoining genomic regions of drought tolerant varieties were closely related and grouped together in the phylogenetic analysis. Moreover, ecotype specific differentiation and greater nucleotide difference with wild relatives was also observed for DECUSSATE gene in rice. This finding indicates differential evolution of qDTY12.1 regions for upland and drought tolerance and omnigenic effect of NCED2T gene in qDTY12.1. Further, we propose a breeding model for enhancing genetic gain for yield under severe drought stress by incorporation of NCEDT, qDTY12.1 and other drought tolerant QTLs for membrane stability in rice.

THE ESTIMATION OF HEAT AND DROUGHT TOLERANCE MAIZE LINES USING DNA MARKERS

The main factor which causes to decrease maize grain yield is drought. In most regions where maize is grown, the water stress during the growing period is caused by both lack of soil moisture and high air temperature. The purposes of our study were the estimation and selection of maize lines for drought and heat tolerance based on DNA markers and determination of the correlation between CAPS markers and plant ability to resist the water stress. As the result of study, the significant differences were found between leaf temperature of maize lines which contained favorable alleles by both CAPS markers in 2018 and 2019 (35.72 and 34.41ºC respectively), LSD0.05=1.27. The leaf temperature of maize lines which had SNP (A) by dhn С397 (36.95ºC) differenced significantly with lines contained favorable allele by rspC1090 or lines with no favorable alleles in 2018 (33.68 and 34.35ºC respectively). Based on analysis by seeds germinating in sucrose solution the significant differences were observed between the amount of sprouted seeds in lines contained SNP(G) by rspC1090 and lines without any favorable allele (4% and 2.25% respectively), LSD0.05= 1.70. As the result of correlation analysis, the positive correlation was determined between SNP(A) by dhnС397 marker in maize lines and leaf temperature in 2018-2019 (r=0.16). The positive correlation was observed between SNP(G)byrspC1090 and the percent of sprouted seeds in sucrose solution (r=0.31). Thus, for complex estimation and maize line selection for drought and heat tolerance it could be recommended to use two CAPS markers dhnC397 and rspC1090.

Incorporating selfing to purge deleterious alleles in a cassava genomic selection program

Cassava has been found to carry high levels of recessive deleterious mutations and it is known to suffer from inbreeding depression. Breeders therefore consider specific approaches to decrease cassava’s genetic load. Using self fertilization to unmask deleterious recessive alleles and therefore accelerate their purging is one possibility. Before implementation of this approach we sought to understand better its consequences through simulation. Founder populations with high directional dominance were simulated using a natural selection forward simulator. The founder population was then subjected to five generations of genomic selection in schemes that did or did not include a generation of phenotypic selection on selfed progeny. We found that genomic selection was less effective under the directional dominance model than under the additive models that have commonly been used in simulations. While selection did increase favorable allele frequencies, increased inbreeding during selection caused decreased gain in genotypic values under the directional dominance. While purging selection on selfed individuals was effective in the first breeding cycle, it was not effective in later cycles, an effect we attributed to the fact that the generation of selfing decreased the relatedness of the genomic prediction training population from selection candidates. That decreased relatedness caused genomic prediction accuracy to be lower in schemes incorporating selfing. We found that selection on individuals partially inbred by one generation of selfing did increase mean genetic value of the partially inbred population, but that this gain was accompanied by a relatively small increase in favorable allele frequencies such that improvement in the outbred population was lower than might have been intuited.

Hitchhiking and Selective Sweeps

When a favorable allele increases in frequency, it alters the coalescent structure (the pattern of times back to a common ancestor) at linked sites relative to that under drift. This creates patterns of sequence polymorphism than can be used to potentially detect ongoing, or very recent, selection. This idea of a neutral allele hitchhiking up to high frequency when coupled to a favorable allele is the notion of a selective sweep, and this chapter reviews the considerable body of associated population-genetics theory on sweeps. Different types of sweeps leave different signatures, resulting in the very diverse collection of tests of selection discussed in Chapter 9. Either a history of recurrent sweeps, or of background selection, results in linked genomic regions of reduced effective population size. This implies that more mutations in sich regions are efficiently neutral, which can result in increased substitution rates and lower codon bias. Finally, the chapter examines the theory for when response is expected to start from existing variation, as opposed to waiting for the appearance of new mutations.